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Kaushal JB, Raut P, Muniyan S, Siddiqui JA, Alsafwani ZW, Seshacharyulu P, Nair SS, Tewari AK, Batra SK. Racial disparity in prostate cancer: an outlook in genetic and molecular landscape. Cancer Metastasis Rev 2024:10.1007/s10555-024-10193-8. [PMID: 38902476 DOI: 10.1007/s10555-024-10193-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 06/04/2024] [Indexed: 06/22/2024]
Abstract
Prostate cancer (PCa) incidence, morbidity, and mortality rates are significantly impacted by racial disparities. Despite innovative therapeutic approaches and advancements in prevention, men of African American (AA) ancestry are at a higher risk of developing PCa and have a more aggressive and metastatic form of the disease at the time of initial PCa diagnosis than other races. Research on PCa has underlined the biological and molecular basis of racial disparity and emphasized the genetic aspect as the fundamental component of racial inequality. Furthermore, the lower enrollment rate, limited access to national-level cancer facilities, and deferred treatment of AA men and other minorities are hurdles in improving the outcomes of PCa patients. This review provides the most up-to-date information on various biological and molecular contributing factors, such as the single nucleotide polymorphisms (SNPs), mutational spectrum, altered chromosomal loci, differential gene expression, transcriptome analysis, epigenetic factors, tumor microenvironment (TME), and immune modulation of PCa racial disparities. This review also highlights future research avenues to explore the underlying biological factors contributing to PCa disparities, particularly in men of African ancestry.
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Affiliation(s)
- Jyoti B Kaushal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Pratima Raut
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Sakthivel Muniyan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Jawed A Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Zahraa W Alsafwani
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Parthasarathy Seshacharyulu
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Sujit S Nair
- Department of Urology and the Tisch Cancer Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ashutosh K Tewari
- Department of Urology and the Tisch Cancer Institute at the Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA.
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE-68198, USA.
- Division of Urology, Department of Surgery, University of Nebraska Medical Center, Omaha, NE-68198, USA.
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE-68198, USA.
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Gong J, Kim DM, Freeman MR, Kim H, Ellis L, Smith B, Theodorescu D, Posadas E, Figlin R, Bhowmick N, Freedland SJ. Genetic and biological drivers of prostate cancer disparities in Black men. Nat Rev Urol 2024; 21:274-289. [PMID: 37964070 DOI: 10.1038/s41585-023-00828-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2023] [Indexed: 11/16/2023]
Abstract
Black men with prostate cancer have historically had worse outcomes than white men with prostate cancer. The causes of this disparity in outcomes are multi-factorial, but a potential basis is that prostate cancers in Black men are biologically distinct from prostate cancers in white men. Evidence suggests that genetic and ancestral factors, molecular pathways involving androgen and non-androgen receptor signalling, inflammation, epigenetics, the tumour microenvironment and tumour metabolism are contributing factors to the racial disparities observed. Key genetic and molecular pathways linked to prostate cancer risk and aggressiveness have potential clinical relevance. Describing biological drivers of prostate cancer disparities could inform efforts to improve outcomes for Black men with prostate cancer.
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Affiliation(s)
- Jun Gong
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Daniel M Kim
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Michael R Freeman
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hyung Kim
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Leigh Ellis
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bethany Smith
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dan Theodorescu
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Edwin Posadas
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Robert Figlin
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Neil Bhowmick
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stephen J Freedland
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Section of Urology, Durham VA Medical Center, Durham, NC, USA
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3
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Ferrari MG, Jimenez-Uribe AP, Wang L, Hoeppner LH, Murugan P, Hahm E, Yu J, Kuzel TM, Gradilone SA, Mansini AP. Myeloid differentiation factor-2/LY96, a potential predictive biomarker of metastasis and poor outcomes in prostate cancer: clinical implications as a potential therapeutic target. Oncogene 2024; 43:484-494. [PMID: 38135694 PMCID: PMC10857939 DOI: 10.1038/s41388-023-02925-x] [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: 05/22/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023]
Abstract
Prostate cancer (CaP) is the most diagnosed cancer in males and the second leading cause of cancer deaths. Patients with localized tumors are generally curable. However, no curative treatment exists for patients with advanced and metastatic disease. Therefore, identifying critical proteins involved in the metastatic process would help to develop new therapeutic options for patients with advanced and aggressive CaP. We provide strong evidence that Myeloid differentiation factor-2 (MD2) plays a critical role in metastasis and CaP progression. Analysis of tumor genomic data showed that amplifications of MD2 and increased expression are associated with poor outcomes in patients. Immunohistochemistry analysis of tumor tissues showed a correlation between the expression of MD2 and cancer progression. The Decipher-genomic test validated the potential of MD2 in predicting metastasis. In vitro studies demonstrated that MD2 confers invasiveness by activating MAPK and NF-kB signaling pathways and inducing epithelial-mesenchymal transition. Furthermore, we show that metastatic cells release MD2 (sMD2). We measured serum-sMD2 in patients and found that the level is correlated to disease extent. We determined the significance of MD2 in metastasis in vivo and as a therapeutic target, showing that the molecular and pharmacological targeting of MD2 significantly inhibited metastasis in murine models. We conclude that MD2 predicts metastatic behavior, and serum-MD2 could be studied as a potential non-invasive biomarker for metastasis, whereas MD2 presence on prostate biopsy predicts adverse disease outcome. We suggest MD2-targeted therapies could be developed as potential treatments for aggressive metastatic disease.
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Affiliation(s)
- Marina G Ferrari
- Department of Urology, Rush University Medical Center, Chicago, IL, USA
| | | | - Li Wang
- The Hormel Institute, Masonic Cancer Center, University of Minnesota, Austin, MN, USA
| | - Luke H Hoeppner
- The Hormel Institute, Masonic Cancer Center, University of Minnesota, Austin, MN, USA
| | - Paari Murugan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Eunsil Hahm
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Jindan Yu
- Department of Urology and Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Timothy M Kuzel
- Department of Internal Medicine, Division of Hematology, Oncology and Cell Therapy, Rush Medical College, Chicago, IL, USA
| | | | - Adrian P Mansini
- Department of Urology, Rush University Medical Center, Chicago, IL, USA.
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4
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Ferrari M, Wang L, Hoeppner L, Hahm E, Yu J, Kuzel T, Mansini A. Myeloid differentiation factor-2/LY96, a new predictive biomarker of metastasis in prostate cancer: Clinical implications as a potential therapeutic target. RESEARCH SQUARE 2023:rs.3.rs-2968406. [PMID: 37333086 PMCID: PMC10275058 DOI: 10.21203/rs.3.rs-2968406/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Relapsed prostate cancer (CaP), usually treated with androgen deprivation therapy, acquires resistance to develop into lethal metastatic castration-resistant CaP. The cause of resistance remains elusive, and the lack of biomarkers predictive of castration-resistance emergence is a stumbling block in managing the disease. We provide strong evidence that Myeloid differentiation factor-2 (MD2) plays a critical role in metastasis and CaP progression. Analysis of tumor genomic data and IHC of tumors showed a high frequency of MD2 amplification and association with poor overall survival in patients. The Decipher-genomic test validated the potential of MD2 in predicting metastasis. In vitro studies demonstrated that MD2 confers invasiveness by activating MAPK and NF-kB signaling pathways. Furthermore, we show that metastatic cells release MD2 (sMD2). We measured serum-sMD2 in patients and found that the level is correlated to disease extent. We determined the significance of MD2 as a therapeutic target and found that targeting MD2 significantly inhibited metastasis in a murine model. We conclude that MD2 predicts metastatic behavior and serum-MD2 is a non-invasive biomarker for tumor burden, whereas MD2 presence on prostate biopsy predicts adverse disease outcome. We suggest MD2-targeted therapies could be developed as potential treatments for aggressive metastatic disease.
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Arenas-Gallo C, Owiredu J, Weinstein I, Lewicki P, Basourakos SP, Vince R, Al Hussein Al Awamlh B, Schumacher FR, Spratt DE, Barbieri CE, Shoag JE. Race and prostate cancer: genomic landscape. Nat Rev Urol 2022; 19:547-561. [PMID: 35945369 DOI: 10.1038/s41585-022-00622-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2022] [Indexed: 11/09/2022]
Abstract
In the past 20 years, new insights into the genomic pathogenesis of prostate cancer have been provided. Large-scale integrative genomics approaches enabled researchers to characterize the genetic and epigenetic landscape of prostate cancer and to define different molecular subclasses based on the combination of genetic alterations, gene expression patterns and methylation profiles. Several molecular drivers of prostate cancer have been identified, some of which are different in men of different races. However, the extent to which genomics can explain racial disparities in prostate cancer outcomes is unclear. Future collaborative genomic studies overcoming the underrepresentation of non-white patients and other minority populations are essential.
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Affiliation(s)
- Camilo Arenas-Gallo
- Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Jude Owiredu
- Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
| | - Ilon Weinstein
- Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Patrick Lewicki
- Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
| | - Spyridon P Basourakos
- Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
| | - Randy Vince
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Bashir Al Hussein Al Awamlh
- Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA.,Department of Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Christopher E Barbieri
- Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan E Shoag
- Department of Urology, University Hospitals Cleveland Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA. .,Department of Urology, NewYork-Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA. .,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA.
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Khaliq AM, Erdogan C, Kurt Z, Turgut SS, Grunvald MW, Rand T, Khare S, Borgia JA, Hayden DM, Pappas SG, Govekar HR, Kam AE, Reiser J, Turaga K, Radovich M, Zang Y, Qiu Y, Liu Y, Fishel ML, Turk A, Gupta V, Al-Sabti R, Subramanian J, Kuzel TM, Sadanandam A, Waldron L, Hussain A, Saleem M, El-Rayes B, Salahudeen AA, Masood A. Refining colorectal cancer classification and clinical stratification through a single-cell atlas. Genome Biol 2022; 23:113. [PMID: 35538548 PMCID: PMC9092724 DOI: 10.1186/s13059-022-02677-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/21/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) consensus molecular subtypes (CMS) have different immunological, stromal cell, and clinicopathological characteristics. Single-cell characterization of CMS subtype tumor microenvironments is required to elucidate mechanisms of tumor and stroma cell contributions to pathogenesis which may advance subtype-specific therapeutic development. We interrogate racially diverse human CRC samples and analyze multiple independent external cohorts for a total of 487,829 single cells enabling high-resolution depiction of the cellular diversity and heterogeneity within the tumor and microenvironmental cells. RESULTS Tumor cells recapitulate individual CMS subgroups yet exhibit significant intratumoral CMS heterogeneity. Both CMS1 microsatellite instability (MSI-H) CRCs and microsatellite stable (MSS) CRC demonstrate similar pathway activations at the tumor epithelial level. However, CD8+ cytotoxic T cell phenotype infiltration in MSI-H CRCs may explain why these tumors respond to immune checkpoint inhibitors. Cellular transcriptomic profiles in CRC exist in a tumor immune stromal continuum in contrast to discrete subtypes proposed by studies utilizing bulk transcriptomics. We note a dichotomy in tumor microenvironments across CMS subgroups exists by which patients with high cancer-associated fibroblasts (CAFs) and C1Q+TAM content exhibit poor outcomes, providing a higher level of personalization and precision than would distinct subtypes. Additionally, we discover CAF subtypes known to be associated with immunotherapy resistance. CONCLUSIONS Distinct CAFs and C1Q+ TAMs are sufficient to explain CMS predictive ability and a simpler signature based on these cellular phenotypes could stratify CRC patient prognosis with greater precision. Therapeutically targeting specific CAF subtypes and C1Q + TAMs may promote immunotherapy responses in CRC patients.
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Affiliation(s)
- Ateeq M Khaliq
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Cihat Erdogan
- Isparta University of Applied Sciences, Isparta, Turkey
| | - Zeyneb Kurt
- Northumbria University, Newcastle Upon Tyne, UK
| | | | | | - Tim Rand
- Tempus Labs, Inc., Chicago, IL, USA
| | | | | | | | - Sam G Pappas
- Rush University Medical Center, Chicago, IL, USA
| | | | - Audrey E Kam
- Rush University Medical Center, Chicago, IL, USA
| | | | | | - Milan Radovich
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yong Zang
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yingjie Qiu
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yunlong Liu
- Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Anita Turk
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Vineet Gupta
- Rush University Medical Center, Chicago, IL, USA
| | - Ram Al-Sabti
- Rush University Medical Center, Chicago, IL, USA
| | | | | | | | - Levi Waldron
- CUNY Graduate School of Public Health and Health Policy, New York, NY, USA
| | - Arif Hussain
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | | | - Bassel El-Rayes
- University of Alabama, O'Neil Comprehensive Cancer Institute, Birmingham, AL, USA
| | | | - Ashiq Masood
- Indiana University School of Medicine, Indianapolis, IN, USA.
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Yin T, Zhao H. miR-152-3p impedes the malignant phenotypes of hepatocellular carcinoma by repressing roundabout guidance receptor 1. Cell Mol Biol Lett 2022; 27:22. [PMID: 35236289 PMCID: PMC8903719 DOI: 10.1186/s11658-022-00322-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/09/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND miR-152-3p functions as a tumour suppressor in the progression of hepatic tumorigenesis. Herein, we further discussed the prognostic significance and immune infiltration of miR-152-3p and its potential gene target in hepatocellular carcinoma (HCC). METHODS The Cancer Genome Atlas (TCGA), Integrative Molecular Database of Hepatocellular Carcinoma (HCCDB), Human Protein Atlas (HPA) and Kaplan-Meier Plotter databases were used to evaluate miR-152-3p and roundabout guidance receptor 1 (ROBO1) expression, prognosis and immune infiltration. In vitro cell experiments, including cell proliferation and apoptosis, were evaluated using Cell Counting Kit 8 (CCK8) and terminal-deoxynucleotidyl transferase-mediated nick end labelling (TUNEL) assays. RESULTS Up-regulation of ROBO1 functioned as an oncogene associated with poor prognosis, immune cell enrichment and cell proliferation in HCC. ROBO1 was significantly positively correlated with the enrichment of multiple immune cells and their biomarkers. Enrichment of type-2 T-helper (Th2) cells is an unfavourable biomarker of HCC prognosis. GSEA revealed that ROBO1 correlated with apoptosis, mitosis and carcinogenic signalling pathways. Suppression of cell proliferation and the enhancement of cell apoptosis by miR-152-3p mimics were counteracted by overexpression of ROBO1 in HCC cells. CONCLUSION ROBO1 expression is positively correlated with multiple immune checkpoint molecules, suggesting that ROBO1 may be a potential drug target to enhance the potency of immunotherapy. The miR-152-3p/ROBO1 signalling axis contributes to malignant progression and provides a prospective immunotherapeutic target for HCC.
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Affiliation(s)
- Tao Yin
- Department of General Surgery, Affiliated Hospital of Chifeng University, No. 42 Wangfu Street, Songshan, Chifeng, 024005, China.
| | - Haonan Zhao
- Department of General Surgery, Affiliated Hospital of Chifeng University, No. 42 Wangfu Street, Songshan, Chifeng, 024005, China
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Kim SH, Kim TJ, Shin D, Hur KJ, Hong SH, Lee JY, Ha US. ROBO1 protein expression is independently associated with biochemical recurrence in prostate cancer patients who underwent radical prostatectomy in Asian patients. Gland Surg 2021; 10:2956-2965. [PMID: 34804883 DOI: 10.21037/gs-21-406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 09/03/2021] [Indexed: 11/06/2022]
Abstract
Background The purpose of this study is to investigate the correlation between ROBO1 expression and prostate cancer aggressiveness. Methods ROBO1 expression was evaluated in normal prostate epithelial cells (PrEC) and different prostate cancer cell lines by Western blot analysis. The migration and invasion of native and ROBO1 knockdown cells were evaluated using migration chambers and a Matrigel-coated membrane, respectively. Samples from 145 patients who underwent radical prostatectomy between June 2000 and June 2008, were retrieved from the paraffin files for tissue microarray (TMA) with immunohistochemical analysis. Biochemical recurrence (BCR)-free survival curves were estimated using the Kaplan-Meier and Cox regression methods in two groups of patients classified according to the degree of ROBO1 expression (low or high expression). Results ROBO1 is highly expressed in the prostate cancer cell lines. All ROBO1 knockdown cells (PC3, 22Rv1 and DU 145) showed markedly decreased migration and invasiveness compared to native cells. In 145 patients with radical prostatectomy, the Kaplan-Meier curves and log-rank test for BCR-free survival stratified by ROBO1 expression in organ-confined (pT2) or not (pT3), showed significant differences in 10-year survival between the ROBO1 high and low expression groups (87.2% versus 52.6% in pT2; P=0.047, 51.0% versus 36.9% in pT3; P=0.033). The multivariable-adjusted model showed a markedly increased hazard ratio (HR) in patients with high ROBO1 expression compared to the patients with low ROBO1expression in every model. Conclusions ROBO1 may play an important role in the migration and invasion of prostate cancer cells, and was independently associated with BCR.
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Affiliation(s)
- Sang Hoon Kim
- Department of Urology, Eunpyeong St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Tae-Jung Kim
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dongho Shin
- Department of Urology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kyung Jae Hur
- Department of Urology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sung-Hoo Hong
- Department of Urology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ji Youl Lee
- Department of Urology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - U-Syn Ha
- Department of Urology, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.,Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Liang L, Huang Q, Gan M, Jiang L, Yan H, Lin Z, Zhu H, Wang R, Hu K. High SEC61G expression predicts poor prognosis in patients with Head and Neck Squamous Cell Carcinomas. J Cancer 2021; 12:3887-3899. [PMID: 34093796 PMCID: PMC8176234 DOI: 10.7150/jca.51467] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 04/23/2021] [Indexed: 01/11/2023] Open
Abstract
Background: Overexpression of the membrane protein SEC61 translocon gamma subunit (SEC61G) has been observed in a variety of cancers; however, its role in head and neck squamous cell carcinomas (HNSCC) is unknown. This study aimed to elucidate the relationship between SEC61G and HNSCC based on data from The Cancer Genome Atlas (TCGA) database. Methods: Data for HNSCC patients were collected from TCGA and the expression level of SEC61G was compared between paired HNSCC and normal tissues using the Wilcoxon rank-sum test. The relationship between clinicopathologic features and SEC61G expression was also analyzed using the Wilcoxon rank-sum test and logistic regression. Receiver operating characteristic (ROC) curves were generated to evaluate the value of SEC61G as a binary classifier using the area under the curve (AUC value). The association of clinicopathologic characteristics with prognosis in HNSCC patients was assessed using Cox regression and the Kaplan-Meier methods. A nomogram, based on Cox multivariate analysis, was used to predict the impact of SEC61G on prognosis. Functional enrichment analysis was performed to determine the hallmark pathways associated with differentially expressed genes in HNSCC patients exhibiting high and low SEC61G expression. Results: The expression of SEC61G was significantly elevated in HNSCC tissues compared to normal tissues (P < 0.001). The high expression of SEC61G was significantly correlated with the T stage, M stage, clinical stage, TP53 mutation status, PIK3CA mutation status, primary therapy outcome, and cervical lymph node dissection (all P < 0.05). Meanwhile, ROC curves suggested the significant diagnostic ability of SEC61G for HNSCC (AUC = 0.923). Kaplan-Meier survival analysis showed that patients with HNSCC characterized by high SEC61G expression had a poorer prognosis than patients with low SEC61G expression (hazard ratio = 1.95, 95% confidence interval 1.48-2.56, P < 0.001). Univariate and multivariate analyses revealed that SEC61G was independently associated with overall survival (P = 0.027). Functional annotations indicated that SEC61G is involved in pathways related to translation and regulation of SLITs/ROBOs expression, SRP-dependent co-translational protein targeting to the membrane, nonsense-mediated decay, oxidative phosphorylation, and Parkinson's disease. Conclusion: SEC61G plays a vital role in HNSCC progression and prognosis; it may, therefore, serve as an effective biomarker for the prediction of patient survival.
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Affiliation(s)
- Leifeng Liang
- Department of Oncology, The Sixth Affiliated Hospital of Guangxi Medical University, Yulin, Guangxi, China
| | - Qingwen Huang
- Department of Pathology, The Sixth Affiliated Hospital of Guangxi Medical University, Yulin, Guangxi, China
| | - Mei Gan
- Department of Oncology, The Sixth Affiliated Hospital of Guangxi Medical University, Yulin, Guangxi, China
| | - Liujun Jiang
- Department of Oncology, The Sixth Affiliated Hospital of Guangxi Medical University, Yulin, Guangxi, China
| | - Haolin Yan
- Department of Oncology, The Sixth Affiliated Hospital of Guangxi Medical University, Yulin, Guangxi, China
| | - Zhan Lin
- Department of Oncology, The Sixth Affiliated Hospital of Guangxi Medical University, Yulin, Guangxi, China
| | - Haisheng Zhu
- Department of Oncology, The Sixth Affiliated Hospital of Guangxi Medical University, Yulin, Guangxi, China
| | - Rensheng Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Kai Hu
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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10
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Chen Q, Shen P, Ge WL, Yang TY, Wang WJ, Meng LD, Huang XM, Zhang YH, Cao SJ, Miao Y, Jiang KR, Zhang JJ. Roundabout homolog 1 inhibits proliferation via the YY1-ROBO1-CCNA2-CDK2 axis in human pancreatic cancer. Oncogene 2021; 40:2772-2784. [PMID: 33714986 DOI: 10.1038/s41388-021-01741-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 02/18/2021] [Accepted: 02/26/2021] [Indexed: 01/31/2023]
Abstract
Pancreatic cancer (PC) is highly malignant and has a high mortality with a 5-year survival rate of less than 8%. As a member of the roundabout immunoglobulin superfamily of proteins, ROBO1 plays an important role in embryogenesis and organogenesis and also inhibits metastasis in PC. Our study was designed to explore whether ROBO1 has effects on the proliferation of PC and its specific mechanism. The expression of ROBO1 was higher in cancer tissues than in matched adjacent tissues by immunohistochemistry (IHC) and qRT-PCR. Low ROBO1 expression is associated with PC progression and poor prognosis. Overexpression of ROBO1 can inhibit the proliferation of PC cells in vitro, and the S phase fraction can also be induced. Further subcutaneous tumor formation in nude mice showed that ROBO1 overexpression can significantly inhibit tumor growth. YY1 was found to directly bind to the promoter region of ROBO1 to promote transcription by a luciferase reporter gene assay, a chromatin immunoprecipitation (ChIP) and an electrophoretic mobility shift assay (EMSA). Mechanistic studies showed that YY1 can inhibit the development of PC by directly regulating ROBO1 via the CCNA2/CDK2 axis. Taken together, our results suggest that ROBO1 may be involved in the development and progression of PC by regulating cell proliferation and shows that ROBO1 may be a novel and promising therapeutic target for PC.
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Affiliation(s)
- Qun Chen
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Peng Shen
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Wan-Li Ge
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Tao-Yue Yang
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Wu-Jun Wang
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Ling-Dong Meng
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Xu-Min Huang
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Yi-Han Zhang
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Shou-Ji Cao
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Yi Miao
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Kui-Rong Jiang
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
- Pancreas Institute, Nanjing Medical University, Nanjing, China.
| | - Jing-Jing Zhang
- Pancreas Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
- Pancreas Institute, Nanjing Medical University, Nanjing, China.
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11
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Lin HY, Wang X, Tseng TS, Kao YH, Fang Z, Molina PE, Cheng CH, Berglund AE, Eeles RA, Muir KR, Pashayan N, Haiman CA, Brenner H, Consortium TP, Park JY. Alcohol Intake and Alcohol-SNP Interactions Associated with Prostate Cancer Aggressiveness. J Clin Med 2021; 10:553. [PMID: 33540941 PMCID: PMC7867322 DOI: 10.3390/jcm10030553] [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: 12/03/2020] [Revised: 01/25/2021] [Accepted: 01/28/2021] [Indexed: 12/24/2022] Open
Abstract
Excessive alcohol intake is a well-known modifiable risk factor for many cancers. It is still unclear whether genetic variants or single nucleotide polymorphisms (SNPs) can modify alcohol intake's impact on prostate cancer (PCa) aggressiveness. The objective is to test the alcohol-SNP interactions of the 7501 SNPs in the four pathways (angiogenesis, mitochondria, miRNA, and androgen metabolism-related pathways) associated with PCa aggressiveness. We evaluated the impacts of three excessive alcohol intake behaviors in 3306 PCa patients with European ancestry from the PCa Consortium. We tested the alcohol-SNP interactions using logistic models with the discovery-validation study design. All three excessive alcohol intake behaviors were not significantly associated with PCa aggressiveness. However, the interactions of excessive alcohol intake and three SNPs (rs13107662 [CAMK2D, p = 6.2 × 10-6], rs9907521 [PRKCA, p = 7.1 × 10-5], and rs11925452 [ROBO1, p = 8.2 × 10-4]) were significantly associated with PCa aggressiveness. These alcohol-SNP interactions revealed contrasting effects of excessive alcohol intake on PCa aggressiveness according to the genotypes in the identified SNPs. We identified PCa patients with the rs13107662 (CAMK2D) AA genotype, the rs11925452 (ROBO1) AA genotype, and the rs9907521 (PRKCA) AG genotype were more vulnerable to excessive alcohol intake for developing aggressive PCa. Our findings support that the impact of excessive alcohol intake on PCa aggressiveness was varied by the selected genetic profiles.
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Affiliation(s)
- Hui-Yi Lin
- Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Xinnan Wang
- Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Tung-Sung Tseng
- Behavioral and Community Health Sciences Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Yu-Hsiang Kao
- Behavioral and Community Health Sciences Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Zhide Fang
- Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Patricia E Molina
- Department of Physiology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
- Comprehensive Alcohol Research Center, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Chia-Ho Cheng
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Anders E Berglund
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Rosalind A Eeles
- The Institute of Cancer Research, and The Royal Marsden NHS Foundation Trust, London, SM2 5NG, UK
| | - Kenneth R Muir
- Division of Population Health, Health Services Research, and Primary Care, University of Manchester, Oxford Road, Manchester, M139PT, UK
| | - Nora Pashayan
- Department of Applied Health Research, University College London, WC1E 7HB, London, UK
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA 90015, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), D-69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
| | - The Practical Consortium
- The Prostate Cancer Association Group to Investigate Cancer Associated Alterations in the Genome Consortium (PRACTICAL, http://practical.icr.ac.uk/), London SM2 5NG, UK. Additional members from The PRACTICAL Consortium were provided in the Supplement
| | - Jong Y Park
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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12
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Siddique HR. Meet Our Editorial Board Member. Recent Pat Anticancer Drug Discov 2020. [DOI: 10.2174/157489281504201208101651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Hifzur R. Siddique
- Section of Genetics Department of Zoology Aligarh Muslim University Aligarh, India
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13
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Ferrari MG, Ganaie AA, Shabenah A, Mansini AP, Wang L, Murugan P, Davicioni E, Wang J, Deng Y, Hoeppner LH, Warlick CA, Konety BR, Saleem M. Identifying and treating ROBO1 -ve /DOCK1 +ve prostate cancer: An aggressive cancer subtype prevalent in African American patients. Prostate 2020; 80:1045-1057. [PMID: 32687658 PMCID: PMC7556361 DOI: 10.1002/pros.24018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/15/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND There is a need to develop novel therapies which could be beneficial to patients with prostate cancer (CaP) including those who are predisposed to poor outcome, such as African-Americans. This study investigates the role of ROBO1-pathway in predicting outcome and race-based disparity in patients with CaP. METHODS AND RESULTS Aided by RNA sequencing-based DECIPHER-testing and immunohistochemical (IHC) analysis of tumors we show that ROBO1 is lost during the progressive stages of CaP, a prevalent feature in African-Americans. We show that the loss of ROBO1 predicts high-risk of recurrence, metastasis and poor outcome of androgen-deprivation therapy in radical prostatectomy-treated patients. These data identified an aggressive ROBO1deficient /DOCK1+ve sub-class of CaP. Combined genetic and IHC data showed that ROBO1 loss is accompanied by DOCK1/Rac1 elevation in grade-III/IV primary-tumors and Mets. We observed that the hypermethylation of ROBO1-promoter contributes to loss of expression that is highly prevalent in African-Americans. Because of limitations in restoring ROBO1 function, we asked if targeting the DOCK1 could be an ideal strategy to inhibit progression or treat ROBO1deficient metastatic-CaP. We tested the pharmacological efficacy of CPYPP, a selective inhibitor of DOCK1 under in vitro and in vivo conditions. Using ROBO1-ve and ROBO1+ve CaP models, we determined the median effective concentration of CPYPP for growth. DOCK1-inhibitor treatment significantly decreased the (a) Rac1-GTP/β-catenin activity, (b) transmigration of ROBO1deficient cells across endothelial lining, and (c) metastatic spread of ROBO1deficient cells through the vasculature of transgenicfl Zebrafish model. CONCLUSION We suggest that ROBO1 status forms as predictive biomarker of outcome in high-risk populations such as African-Americans and DOCK1-targeting therapy has a clinical potential for treating metastatic-CaP.
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Affiliation(s)
- Marina G. Ferrari
- Department of Urology, School of Medicine, Masonic Cancer Center, University of Minnesota
| | - Arsheed A. Ganaie
- Department of Urology, School of Medicine, Masonic Cancer Center, University of Minnesota
| | - Ashraf Shabenah
- Institute for Health Informatics, Masonic Cancer Center, University of Minnesota
| | - Adrian P. Mansini
- Department of Urology, School of Medicine, Masonic Cancer Center, University of Minnesota
| | - Li Wang
- Hormel Institute, University of Minnesota, Austin, MN
| | - Paari Murugan
- Department of Laboratory Medicine and Pathology, University of Minnesota
| | | | - Jinhua Wang
- Institute for Health Informatics, Masonic Cancer Center, University of Minnesota
| | - Yibin Deng
- Department of Urology, School of Medicine, Masonic Cancer Center, University of Minnesota
| | | | - Christopher A. Warlick
- Department of Urology, School of Medicine, Masonic Cancer Center, University of Minnesota
| | - Badrinath R. Konety
- Department of Urology, School of Medicine, Masonic Cancer Center, University of Minnesota
| | - Mohammad Saleem
- Department of Urology, School of Medicine, Masonic Cancer Center, University of Minnesota
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14
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Song Q, Zhang H, He J, Kong H, Tao R, Huang Y, Yu H, Zhang Z, Huang Z, Wei L, Liu C, Wang L, Ning Q, Huang J. Long non-coding RNA LINC00473 acts as a microRNA-29a-3p sponge to promote hepatocellular carcinoma development by activating Robo1-dependent PI3K/AKT/mTOR signaling pathway. Ther Adv Med Oncol 2020; 12:1758835920937890. [PMID: 32922520 PMCID: PMC7457704 DOI: 10.1177/1758835920937890] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Long non-coding RNAs have suppressive or oncogenic effects in various types
of cancers by serving as competing endogenous RNAs for specific microRNAs.
In the present study, we aim to delineate the underlying mechanism by which
the LINC00473/miR-29a-3p/Robo1 axis affects cell proliferation, migration,
invasion, and metastasis in hepatocellular carcinoma (HCC). Methods: The level of Robo1 was examined in HCC tissues and cells, along with its
regulatory effects on proliferation, migration, and invasion of HCC cells.
Afterwards, the possible involvement of the PI3K/AKT/mTOR signaling pathway
was determined. Next, miR-29a-3p expression was overexpressed or inhibited
to investigate its regulatory role on HCC cell activities. The interaction
among miR-29a-3p, Robo1, and LINC00473 was further characterized. Finally, a
xenograft tumor in nude mice was conducted to measure tumorigenesis and
metastasis in vivo. Results: miR-29a-3p was downregulated while Robo1 was upregulated in HCC tissues and
cells. miR-29a-3p targeted Robo1 and negatively regulated its expression. In
response to miR-29a-3p overexpression, Robo1 silencing or LINC00473
silencing, HCC cell proliferation, migration, invasion, tumor progression,
and metastasis were impeded, which was involved with the inactivation of the
PI3K/AKT/mTOR signaling pathway. Notably, LINC00473 could competitively bind
to miR-29a-3p to upregulate Robo1 expression. Conclusion: LINC00473 might be involved in HCC progression by acting as a miR-29a-3p
sponge to upregulate the expression of Robo1 that activates the
PI3K/AKT/mTOR signaling pathway, which leads to enhanced cell proliferation,
migration, invasion, tumor progression, and metastasis in HCC.
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Affiliation(s)
- Qiqin Song
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Hongyue Zhang
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Jinan He
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Hongyan Kong
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Ran Tao
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Yu Huang
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Haijing Yu
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Zhongwei Zhang
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Zhiyong Huang
- Department of Hepatobiliary Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Lai Wei
- Department of Organ Transplant, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Chenghai Liu
- Institute of Liver Disease, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, P. R. China
| | - Likui Wang
- Savaid Medical School, University of Chinese Academy of Science Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Qin Ning
- Department and Institute of Infectious Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P. R. China
| | - Jiaquan Huang
- Department and Institute of Infection Disease, Tongji Hospital, Tongji Medical College, Huazhong University of Science Technology, No. 1095 JieFang Avenue, Wuhan 430030, Hubei Province, P. R. China
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15
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Baker MJ, Cooke M, Kreider-Letterman G, Garcia-Mata R, Janmey PA, Kazanietz MG. Evaluation of active Rac1 levels in cancer cells: A case of misleading conclusions from immunofluorescence analysis. J Biol Chem 2020; 295:13698-13710. [PMID: 32817335 DOI: 10.1074/jbc.ra120.013919] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/23/2020] [Indexed: 12/16/2022] Open
Abstract
A large number of aggressive cancer cell lines display elevated levels of activated Rac1, a small GTPase widely implicated in cytoskeleton reorganization, cell motility, and metastatic dissemination. A commonly accepted methodological approach for detecting Rac1 activation in cancer cells involves the use of a conformation-sensitive antibody that detects the active (GTP-bound) Rac1 without interacting with the GDP-bound inactive form. This antibody has been extensively used in fixed cell immunofluorescence and immunohistochemistry. Taking advantage of prostate and pancreatic cancer cell models known to have high basal Rac1-GTP levels, here we have established that this antibody does not recognize Rac1 but rather detects the intermediate filament protein vimentin. Indeed, Rac1-null PC3 prostate cancer cells or cancer models with low levels of Rac1 activation still show a high signal with the anti-Rac1-GTP antibody, which is lost upon silencing of vimentin expression. Moreover, this antibody was unable to detect activated Rac1 in membrane ruffles induced by epidermal growth factor stimulation. These results have profound implications for the study of this key GTPase in cancer, particularly because a large number of cancer cell lines with characteristic mesenchymal features show simultaneous up-regulation of vimentin and high basal Rac1-GTP levels when measured biochemically. This misleading correlation can lead to assumptions about the validity of this antibody and inaccurate conclusions that may affect the development of appropriate therapeutic approaches for targeting the Rac1 pathway.
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Affiliation(s)
- Martin J Baker
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - Mariana Cooke
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Medicine, Einstein Medical Center Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | - Paul A Janmey
- Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marcelo G Kazanietz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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16
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Mao Y, Nie Q, Yang Y, Mao G. Identification of co‑expression modules and hub genes of retinoblastoma via co‑expression analysis and protein‑protein interaction networks. Mol Med Rep 2020; 22:1155-1168. [PMID: 32468072 PMCID: PMC7339782 DOI: 10.3892/mmr.2020.11189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 04/01/2020] [Indexed: 12/14/2022] Open
Abstract
Retinoblastoma is a common intraocular malignant tumor in children. However, the molecular and genetic mechanisms of retinoblastoma remain unclear. The gene expression dataset GSE110811 was retrieved from Gene Expression Omnibus. After preprocessing, coexpression modules were constructed by weighted gene coexpression network analysis (WGCNA), and modules associated with clinical traits were identified. In addition, functional enrichment analysis was performed for genes in the indicated modules, and protein-protein interaction (PPI) networks and subnetworks were constructed based on these genes. Eight coexpression modules were constructed through WGCNA. Of these, the yellow module had the highest association with severity and age (r=0.82 and P=3e-07; r=0.72 and P=3e-05). The turquoise module had the highest association with months (r=−0.63 and P=5e-04). The genes in the two modules participate in multiple pathways of retinoblastoma, and by combining the PPI network and subnetworks; 10 hub genes were identified in the two modules. The present study identified coexpression modules and hub genes associated with clinical traits of retinoblastoma, providing novel insight into retinoblastoma progression.
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Affiliation(s)
- Yukun Mao
- Department of Orthopedics, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Qingbin Nie
- Department of Neurovascular Surgery, The Third Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing 100039, P.R. China
| | - Yang Yang
- Department of Neurovascular Surgery, The Third Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing 100039, P.R. China
| | - Gengsheng Mao
- Department of Neurovascular Surgery, The Third Medical Centre, Chinese PLA (People's Liberation Army) General Hospital, Beijing 100039, P.R. China
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17
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Umbreen S, Banday MM, Jamroze A, Mansini AP, Ganaie AA, Ferrari MG, Maqbool R, Beigh FH, Murugan P, Morrissey C, Corey E, Konety BR, Saleem M. COMMD3:BMI1 Fusion and COMMD3 Protein Regulate C-MYC Transcription: Novel Therapeutic Target for Metastatic Prostate Cancer. Mol Cancer Ther 2019; 18:2111-2123. [PMID: 31467179 DOI: 10.1158/1535-7163.mct-19-0150] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/24/2019] [Accepted: 08/20/2019] [Indexed: 11/16/2022]
Abstract
Gene rearrangement is reported to be associated to the aggressive phenotype and poor prognosis in prostate cancer. We identified a gene fusion between a transcription repressor (BMI1) and transcriptional factor (COMMD3) in human prostate cancer. We show that COMMD3:BMI1 fusion expression is significantly increased in prostate cancer disease in an order: normal tissue < primary < metastatic tumors (Mets). Although elevated TMPRSS-ERG/ETV fusion is reported in prostate cancer, we identified a subtype of Mets exhibiting low TMPRSS:ETV and high COMMD3:BMI1 We delineated the mechanism and function of COMMD3 and COMMD3:BMI1 in prostate cancer. We show that COMMD3 level is elevated in prostate cancer cell models, PDX models (adenocarcinoma, NECaP), and Mets. The analysis of TCGA/NIH/GEO clinical data showed a positive correlation between increased COMMD3 expression to the disease recurrence and poor survival in prostate cancer. We show that COMMD3 drives proliferation of normal cells and promotes migration/invasiveness of neoplastic cells. We show that COMMD3:BMI1 and COMMD3 regulate C-MYC transcription and C-MYC downstream pathway. The ChIP analysis showed that COMMD3 protein is recruited at the promoter of C-MYC gene. On the basis of these data, we investigated the relevance of COMMD3:BMI1 and COMMD3 as therapeutic targets using in vitro and xenograft mouse models. We show that siRNA-mediated targeting of COMMD3:BMI1 and COMMD3 significantly decreases (i) C-MYC expression in BRD/BET inhibitor-resistant cells, (ii) proliferation/invasion in vitro, and (iii) growth of prostate cancer cell tumors in mice. The IHC analysis of tumors confirmed the targeting of COMMD3-regulated molecular pathway under in vivo conditions. We conclude that COMMD3:BMI1 and COMMD3 are potential progression biomarkers and therapeutic targets of metastatic prostate cancer.
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Affiliation(s)
- Syed Umbreen
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota.,Queens University, Belfast, Northern Ireland
| | - Mudassir Meraj Banday
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Anmbreen Jamroze
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota.,Hormel Institute, Austin, Minnesota
| | - Adrian P Mansini
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Arsheed A Ganaie
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Marina G Ferrari
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Raihana Maqbool
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Firdous H Beigh
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | | | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington
| | - Badrinath R Konety
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota
| | - Mohammad Saleem
- Department of Urology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota.
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18
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Characterization of Novel Murine and Human PDAC Cell Models: Identifying the Role of Intestine Specific Homeobox Gene ISX in Hypoxia and Disease Progression. Transl Oncol 2019; 12:1056-1071. [PMID: 31174057 PMCID: PMC6556561 DOI: 10.1016/j.tranon.2019.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/03/2019] [Accepted: 05/03/2019] [Indexed: 11/23/2022] Open
Abstract
Therapy failure and metastasis-associated mortality are stumbling blocks in the management of PDAC in patients. Failure of therapy is associated to intense hypoxic conditions of tumors. To develop effective therapies, a complete understanding of hypoxia-associated changes in genetic landscape of tumors during disease progression is needed. Because artificially immortalized cell lines do not rightly represent the disease progression, studying genetics of tumors in spontaneous models is warranted. In the current study, we generated a spectrum of spontaneous human (UM-PDC1; UM-PDC2) and murine (HI-PanL, HI-PancI, HI-PanM) models representing localized, invasive, and metastatic PDAC from a patient and transgenic mice (K-rasG12D/Pdxcre/Ink4a/p16-/). These spontaneous models grow vigorously under hypoxia and exhibit activated K-ras signaling, progressive loss of PTEN, and tumorigenicity in vivo. Whereas UM-PDC1 form localized tumors, the UM-PDC2 metastasize to lungs in mice. In an order of progression, these models exhibit genomic instability marked by gross chromosomal rearrangements, centrosome-number variations, Aurora-kinase/H2AX colocalization, loss of primary cilia, and α-tubulin acetylation. The RNA sequencing of hypoxic models followed by qRT-PCR validation and gene-set enrichment identified Intestine-Specific Homeobox factor (ISX)–driven molecular pathway as an indicator PDAC aggressivness. TCGA-PAAD clinical data analysis showed high ISX expression correlation to poor survival of PDAC patients, particularly women. The functional studies showed ISX as a regulator of i) invasiveness and migratory potential and ii) VEGF, MMP2, and NFκB activation in PDAC cells. We suggest that ISX is a potential druggable target and newly developed spontaneous cell models are valuable tools for studying mechanism and testing therapies for PDAC.
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19
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Tong M, Jun T, Nie Y, Hao J, Fan D. The Role of the Slit/Robo Signaling Pathway. J Cancer 2019; 10:2694-2705. [PMID: 31258778 PMCID: PMC6584916 DOI: 10.7150/jca.31877] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/28/2019] [Indexed: 12/25/2022] Open
Abstract
The Slit family is a family of secreted proteins that play important roles in various physiologic and pathologic activities via interacting with Robo receptors. Slit/Robo signaling was first identified in the nervous system, where it functions in neuronal axon guidance; nevertheless, an increasing number of studies have shown that Slit/Robo signaling even regulates other activities, such as angiogenesis, inflammatory cell chemotaxis, tumor cell migration and metastasis. Although the precise role of the ligand-receptor in organisms has been obscure and the conclusions drawn are sometimes paradoxical, tremendous advances in understanding the Slit/Robo signaling pathway have been made. As such, our review summarizes the characteristics of the Slit/Robo signaling pathway and its role in various cell types.
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Affiliation(s)
- Mingfu Tong
- Department of Gastroenterology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China.,State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Tie Jun
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Jianyu Hao
- Department of Gastroenterology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
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20
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Rai R, Yadav SS, Pan H, Khan I, O'Connor J, Alshalalfa M, Davicioni E, Taioli E, Elemento O, Tewari AK, Yadav KK. Epigenetic analysis identifies factors driving racial disparity in prostate cancer. Cancer Rep (Hoboken) 2019; 2:e1153. [PMID: 32721098 DOI: 10.1002/cnr2.1153] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/07/2018] [Accepted: 11/12/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Prostate cancer (PCa) is the second most leading cause of death in men worldwide. African-American men (AA) represent more aggressive form of the disease compared to Caucasian (CA) counterparts. Several lines of evidences suggest that biological factors are responsible for the observed racial disparity. AIM This study was aimed at identifying the epigenetic variation among AA and CA PCa patients and whether DNA methylation differences have an association with clinical outcomes in the two races. METHODS AND RESULTS The cancer genome atlas (TCGA) dataset (2015) was used to identify existing epigenetic variation in AA and CA PCa patients. Reduced Representation Bisulfite Sequencing (RRBS) was performed to identify global DNA methylation changes in a small cohort of AA and CA PCa patients. The RRBS data were then used to identify survival and recurrence outcomes in AA and CA PCa patients using publicly available datasets. The TCGA data analysis revealed epigenetic heterogeneity, which could be categorized into four classes. AA associated primarily to methylation cluster 1 (p = 0.048), and CA associated to methylation cluster 3 (p = 0.000146). Enrichment of the Wnt signaling pathway was identified in both the races; however, they were differentially activated in terms of canonical and non-canonical Wnt signaling. This was further validated using the Decipher Genomics Resource Information Database (GRID). The RRBS data also identified discrete methylation patterns in AA compared with CA and, in part, validated our TCGA findings. Survival analysis using the RRBS data suggested hypomethylated genes to be significantly associated with recurrence of PCa in CA (p = 6.07 × 10-6) as well as in AA (p = 0.0077). CONCLUSION Overall, we observed epigenetic-based racial disparity in PCa which could affect survival and should be considered during prognosis and treatment.
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Affiliation(s)
- Richa Rai
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shalini S Yadav
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Heng Pan
- Department of Physiology and Biophysics, Institute for Precision Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Irtaza Khan
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - James O'Connor
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Elai Davicioni
- GenomeDx Biosciences, Vancouver, British Columbia, Canada
| | - Emanuela Taioli
- Department of Population Health Science and Policy and Institute for Translational Epidemiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Precision Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Ashutosh K Tewari
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kamlesh K Yadav
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, Stamford, Connecticut, USA
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21
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Zheng XB, Liu HS, Zhang LJ, Liu XH, Zhong XL, Zhou C, Hu T, Wu XR, Hu JC, Lian L, Deng QL, Chen YF, Ke J, He XW, Wu XJ, He XS, Lan P. Engulfment and Cell Motility Protein 1 Protects Against DSS-induced Colonic Injury in Mice via Rac1 Activation. J Crohns Colitis 2019; 13:100-114. [PMID: 30219846 DOI: 10.1093/ecco-jcc/jjy133] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND AND AIMS Mucosal healing is an emerging therapeutic goal that could result in clinical remission of inflammatory bowel disease [IBD]. We sought to determine the role of engulfment and cell motility protein 1 [ELMO1] in wound healing in vitro and in vivo and to investigate the underlying pathways. METHODS RNA transcriptome sequencing was performed to detect the expression profiles of mRNA between inflamed tissues and corresponding non-inflamed tissues of IBD patients, followed by Gene Expression Omnibus [GEO] datasets and western blot analysis. The effects of ELMO1 overexpression or knockdown on cell migration and proliferation were determined. The dependence of these effects on Rac1 was assessed using a Rac1 inhibitor [NSC23766] and a Rac1 pull-down assay. We identified the underlying pathways involved by Gene Ontology [GO] analysis. A dextran sulphate sodium [DSS]-induced colitis model was established to evaluate the role of ELMO1 in colonic mucosal healing. RESULTS ELMO1 was upregulated in inflamed tissues compared with corresponding non-inflamed tissues. ELMO1 overexpression increased cell migration in a Rac1-dependent manner. Depletion of ELMO1, or NSC23766 administration, abolished this effect. GO analysis revealed that ELMO1 overexpression preferentially affected pathways involved in cytoskeletal regulation and wound healing, which was demonstrated by enhanced F-actin staining and increased numbers of extending lamellipodia in cells overexpressing ELMO1. In DSS-induced colitis, systemic delivery of pSin-EF2-ELMO1-Pur attenuated colonic inflammation and promoted recovery from colonic injury. The protective effect of ELMO1 was dependent on Rac1 activation. CONCLUSIONS ELMO1 protects against DSS-induced colonic injury in mice through its effect on epithelial migration via Rac1 activation.
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Affiliation(s)
- Xiao-Bin Zheng
- Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hua-Shan Liu
- Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Long-Juan Zhang
- Laboratory of Surgery, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xuan-Hui Liu
- Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiao-Li Zhong
- Joint Cardiac Surgery Center, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Chi Zhou
- Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tuo Hu
- Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xian-Rui Wu
- Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jian-Cong Hu
- Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lei Lian
- Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qi-Ling Deng
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yu-Feng Chen
- Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jia Ke
- Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiao-Wen He
- Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiao-Jian Wu
- Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiao-Sheng He
- Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ping Lan
- Department of Colorectal Surgery, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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22
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Chen W, Ye L, Wen D, Chen F. MiR-490-5p Inhibits Hepatocellular Carcinoma Cell Proliferation, Migration and Invasion by Directly Regulating ROBO1. Pathol Oncol Res 2019; 25:1-9. [PMID: 28924964 DOI: 10.1007/s12253-017-0305-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 09/01/2017] [Indexed: 12/13/2022]
Abstract
Studies have investigated the effect of ROBO1. All the same, the relationship between miR-490-5p and ROBO1, and the underlying mechanism are still unclear. We aimed to study the effect of microRNA-490-5p (miR-490-5p) on hepatocellular carcinoma (HCC) cell proliferation, migration and invasion by directly regulating ROBO1. The expression of miR-490-5p and ROBO1 in HCC tissues and cells were tested by RT-qPCR, and the Hep3B cells were selected for subsequent experiments. We confirmed the relationship between miR-490-5p and ROBO1 by luciferase reporter system. The effects of miR-490-5p on cell proliferation, migration and invasion of Hep3B cells were assessed by MTT assay, colony formation assay, wound healing assay and transwell assay, respectively. Flow cytometry was employed to detect the influence of miR-490-5p on cell cycle and apoptosis of Hep3B cells. The expression of miR-490-5p was down-regulated, while ROBO1 was up-regulated in HCC tissues and cells than the controls. MiR-490-5p can target ROBO1. MiR-490-5p inhibited cell proliferation, migration and invasion, but promoted cell apoptosis of Hep3B cells by inhibiting ROBO1. We confirmed that miR-490-5p could directly suppress ROBO1, which might be a potential mechanism in inhibiting HCC cell proliferation, migration and invasion.
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Affiliation(s)
- Weiqing Chen
- Department of General Surgery, The People's Hospital of Lin'an City, No 548 Yijing Street, Jincheng town, Lin'an City, Zhejiang Province, 311300, China
| | - Lijun Ye
- Department of Gynecology and Obstetrics, The People's Hospital of Lin'an City, Lin'an City, Zhejiang Province, 311300, China
| | - Dengcheng Wen
- Department of General Surgery, The People's Hospital of Lin'an City, No 548 Yijing Street, Jincheng town, Lin'an City, Zhejiang Province, 311300, China
| | - Feihua Chen
- Department of Gynecology and Obstetrics, The People's Hospital of Lin'an City, Lin'an City, Zhejiang Province, 311300, China.
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23
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Zhang C, Xiong J, Yang Q, Wang Y, Shi H, Tian Q, Huang H, Kong D, Lv J, Liu D, Gao X, Zi X, Sun Y. Profiling and bioinformatics analyses of differential circular RNA expression in prostate cancer cells. Future Sci OA 2018; 4:FSOA340. [PMID: 30416748 PMCID: PMC6222276 DOI: 10.4155/fsoa-2018-0046] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/30/2018] [Indexed: 12/13/2022] Open
Abstract
AIM There is little knowledge about the expression profile and function of circular RNAs (circRNAs) in prostate cancer (PCa). METHODS The expression profiles of circRNAs in RWPE-1, 22RV1 and PC3 cells were explored via high-throughput circRNAs sequencing and validated by real-time qPCR. The roles of differentially expressed circRNAs were evaluated by bioinformatics analyses. RESULTS Altogether 9545 circRNAs were identified and hundreds of differentially expressed circRNAs were recognized. CircRNA-miRNA networks analysis showed that many circRNAs, including circSLC7A6, circGUCY1A2 and circZFP57 could cross-talk with tumor-related miRNAs such as miR-21, miR-143 and miR-200 family. CONCLUSION The results of our bioinformatics analyses suggested that circRNAs should play critical roles in the development and progression of PCa.
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Affiliation(s)
- Chunlei Zhang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, PR China
- Department of Urology, Lanzhou General Hospital of PLA, Lanzhou, PR China
| | - Jun Xiong
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, PR China
- Department of Histological Embryology, Second Military Medical University, Shanghai, PR China
| | - Qi Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, PR China
- Department of Urology, Lanzhou General Hospital of PLA, Lanzhou, PR China
| | - Ye Wang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, PR China
| | - Haoqing Shi
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, PR China
| | - Qinqin Tian
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, PR China
| | - Hai Huang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, PR China
| | - Depei Kong
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, PR China
| | - Jianmin Lv
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, PR China
| | - Dan Liu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, PR China
| | - Xu Gao
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, PR China
| | - Xiaoyuan Zi
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, PR China
- Department of Cell Biology, Second Military Medical University, Shanghai, PR China
| | - Yinghao Sun
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, PR China
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24
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Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, Ghori M, Zamora J, Butler A, Whitaker H, Kote-Jarai Z, Alexandrov LB, Van Loo P, Massie CE, Dentro S, Warren AY, Verrill C, Berney DM, Dennis N, Merson S, Hawkins S, Howat W, Lu YJ, Lambert A, Kay J, Kremeyer B, Karaszi K, Luxton H, Camacho N, Marsden L, Edwards S, Matthews L, Bo V, Leongamornlert D, McLaren S, Ng A, Yu Y, Zhang H, Dadaev T, Thomas S, Easton DF, Ahmed M, Bancroft E, Fisher C, Livni N, Nicol D, Tavaré S, Gill P, Greenman C, Khoo V, Van As N, Kumar P, Ogden C, Cahill D, Thompson A, Mayer E, Rowe E, Dudderidge T, Gnanapragasam V, Shah NC, Raine K, Jones D, Menzies A, Stebbings L, Teague J, Hazell S, Corbishley C, de Bono J, Attard G, Isaacs W, Visakorpi T, Fraser M, Boutros PC, Bristow RG, Workman P, Sander C, Hamdy FC, Futreal A, McDermott U, Al-Lazikani B, Lynch AG, Bova GS, Foster CS, Brewer DS, Neal DE, Cooper CS, Eeles RA. Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets. Nat Genet 2018; 50:682-692. [PMID: 29662167 PMCID: PMC6372064 DOI: 10.1038/s41588-018-0086-z] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 02/22/2018] [Indexed: 12/18/2022]
Abstract
Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials.
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Affiliation(s)
- David C Wedge
- Oxford Big Data Institute, University of Oxford, Oxford, UK.
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.
- Oxford NIHR Biomedical Research Centre, Oxford, UK.
| | - Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Thomas Mitchell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - Dan J Woodcock
- Oxford Big Data Institute, University of Oxford, Oxford, UK
| | | | - Mohammed Ghori
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jorge Zamora
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Adam Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Hayley Whitaker
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | | | | | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Cancer Genomics, The Francis Crick Institute, London, UK
| | - Charlie E Massie
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
- Early Detection Programme, Cancer Research UK Cambridge Centre, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Stefan Dentro
- Oxford Big Data Institute, University of Oxford, Oxford, UK
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Cancer Genomics, The Francis Crick Institute, London, UK
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Clare Verrill
- Oxford NIHR Biomedical Research Centre, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Dan M Berney
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Nening Dennis
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Sue Merson
- The Institute of Cancer Research, London, UK
| | - Steve Hawkins
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - William Howat
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Yong-Jie Lu
- Centre for Molecular Oncology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Adam Lambert
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Jonathan Kay
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Barbara Kremeyer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Katalin Karaszi
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Hayley Luxton
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Niedzica Camacho
- Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- The Institute of Cancer Research, London, UK
| | - Luke Marsden
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Lucy Matthews
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Valeria Bo
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Daniel Leongamornlert
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- The Institute of Cancer Research, London, UK
| | - Stuart McLaren
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Anthony Ng
- The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yongwei Yu
- Second Military Medical University, Shanghai, China
| | | | | | - Sarah Thomas
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | | | - Elizabeth Bancroft
- The Institute of Cancer Research, London, UK
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Cyril Fisher
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Naomi Livni
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - David Nicol
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Simon Tavaré
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Pelvender Gill
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | | | - Vincent Khoo
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - Pardeep Kumar
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | - Declan Cahill
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Alan Thompson
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Erik Mayer
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Edward Rowe
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Tim Dudderidge
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Vincent Gnanapragasam
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Nimish C Shah
- Department of Urology, Addenbrooke's Hospital, Cambridge, UK
| | - Keiran Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - David Jones
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Andrew Menzies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Lucy Stebbings
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Jon Teague
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Steven Hazell
- Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | | | | | | | | | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Michael Fraser
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Robert G Bristow
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | | | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA
| | - Freddie C Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Andrew G Lynch
- Statistics and Computational Biology Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
- School of Mathematics and Statistics/School of Medicine, University of St. Andrews, Fife, UK
| | - G Steven Bova
- Johns Hopkins School of Medicine, Baltimore, MD, USA
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | | | - Daniel S Brewer
- The Institute of Cancer Research, London, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich, UK
| | - David E Neal
- Uro-Oncology Research Group, Cancer Research UK, Cambridge Institute, Cambridge, UK
- Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Colin S Cooper
- The Institute of Cancer Research, London, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Rosalind A Eeles
- The Institute of Cancer Research, London, UK.
- Royal Marsden NHS Foundation Trust, London and Sutton, UK.
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25
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Ritchie C, Mack A, Harper L, Alfadhli A, Stork PJS, Nan X, Barklis E. Analysis of K-Ras Interactions by Biotin Ligase Tagging. Cancer Genomics Proteomics 2018. [PMID: 28647697 DOI: 10.21873/cgp.20034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Mutations of the human K-Ras 4B (K-Ras) G protein are associated with a significant proportion of all human cancers. Despite this fact, a comprehensive analysis of K-Ras interactions is lacking. Our investigations focus on characterization of the K-Ras interaction network. MATERIALS AND METHODS We employed a biotin ligase-tagging approach, in which tagged K-Ras proteins biotinylate neighbor proteins in a proximity-dependent fashion, and proteins are identified via mass spectrometry (MS) sequencing. RESULTS In transfected cells, a total of 748 biotinylated proteins were identified from cells expressing biotin ligase-tagged K-Ras variants. Significant differences were observed between membrane-associated variants and a farnesylation-defective mutant. In pancreatic cancer cells, 56 K-Ras interaction partners were identified. Most of these were cytoskeletal or plasma membrane proteins, and many have been identified previously as potential cancer biomarkers. CONCLUSION Biotin ligase tagging offers a rapid and convenient approach to the characterization of K-Ras interaction networks.
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Affiliation(s)
- Christopher Ritchie
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Andrew Mack
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Logan Harper
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A
| | - Philip J S Stork
- Department of Vollum Institute, Oregon Health & Science University, Portland, OR, U.S.A
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, U.S.A
| | - Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, U.S.A.
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Zhao SJ, Shen YF, Li Q, He YJ, Zhang YK, Hu LP, Jiang YQ, Xu NW, Wang YJ, Li J, Wang YH, Liu F, Zhang R, Yin GY, Tang JH, Zhou D, Zhang ZG. SLIT2/ROBO1 axis contributes to the Warburg effect in osteosarcoma through activation of SRC/ERK/c-MYC/PFKFB2 pathway. Cell Death Dis 2018; 9:390. [PMID: 29523788 PMCID: PMC5844886 DOI: 10.1038/s41419-018-0419-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 01/15/2018] [Accepted: 02/14/2018] [Indexed: 12/20/2022]
Abstract
Cellular metabolic reprogramming is the main characteristic of cancer cells and identification of targets using this metabolic pattern is extremely important to treat cancers, such as osteosarcoma (OS). In this study, SLIT2 and ROBO1 were upregulated in OS, and higher expression of ROBO1 was associated with worse overall survival rate. Furthermore, in vitro and in vivo experiments demonstrated that the SLIT2/ROBO1 axis promotes proliferation, inhibits apoptosis, and contributes to the Warburg effect in OS cells. Mechanistically, the SLIT2/ROBO1 axis exerted cancer-promoting effects on OS via activation of the SRC/ERK/c-MYC/PFKFB2 pathway. Taken together, the findings reveal a previously unappreciated function of SLIT2/ROBO1 signaling in OS, which is intertwined with metabolic alterations that promote cancer progression. Targeting the SLIT2/ROBO1 axis may be a potential therapeutic approach for patients with OS.
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Affiliation(s)
- Shu-Jie Zhao
- Department of Orthopedic, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, Jiangsu, China
- Department of Orthopedics, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, 213003, Jiangsu, China
| | - Yi-Fei Shen
- Department of Orthopedics, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, 213003, Jiangsu, China
| | - Qing Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yun-Jie He
- Department of General Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Yun-Kun Zhang
- Department of Orthopedics, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, 213003, Jiangsu, China
| | - Li-Peng Hu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yu-Qing Jiang
- Department of Orthopedics, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, 213003, Jiangsu, China
| | - Nan-Wei Xu
- Department of Orthopedics, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, 213003, Jiangsu, China
| | - Yu-Ji Wang
- Department of Orthopedics, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, 213003, Jiangsu, China
| | - Jun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ya-Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fei Liu
- Department of Obstetrics and Gynecology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Rong Zhang
- Department of Obstetrics and Gynecology, Fengxian Hospital, Southern Medical University, Shanghai, 201499, China
| | - Guo-Yong Yin
- Department of Orthopedic, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, Jiangsu, China
| | - Jin-Hai Tang
- Department of General Surgery, The First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Dong Zhou
- Department of Orthopedics, The Affiliated Hospital of Nanjing Medical University, Changzhou No.2 People's Hospital, Changzhou, 213003, Jiangsu, China.
| | - Zhi-Gang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Myers JS, Vallega KA, White J, Yu K, Yates CC, Sang QXA. Proteomic characterization of paired non-malignant and malignant African-American prostate epithelial cell lines distinguishes them by structural proteins. BMC Cancer 2017; 17:480. [PMID: 28697756 PMCID: PMC5504803 DOI: 10.1186/s12885-017-3462-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 06/28/2017] [Indexed: 11/22/2022] Open
Abstract
Background While many factors may contribute to the higher prostate cancer incidence and mortality experienced by African-American men compared to their counterparts, the contribution of tumor biology is underexplored due to inadequate availability of African-American patient-derived cell lines and specimens. Here, we characterize the proteomes of non-malignant RC-77 N/E and malignant RC-77 T/E prostate epithelial cell lines previously established from prostate specimens from the same African-American patient with early stage primary prostate cancer. Methods In this comparative proteomic analysis of RC-77 N/E and RC-77 T/E cells, differentially expressed proteins were identified and analyzed for overrepresentation of PANTHER protein classes, Gene Ontology annotations, and pathways. The enrichment of gene sets and pathway significance were assessed using Gene Set Enrichment Analysis and Signaling Pathway Impact Analysis, respectively. The gene and protein expression data of age- and stage-matched prostate cancer specimens from The Cancer Genome Atlas were analyzed. Results Structural and cytoskeletal proteins were differentially expressed and statistically overrepresented between RC-77 N/E and RC-77 T/E cells. Beta-catenin, alpha-actinin-1, and filamin-A were upregulated in the tumorigenic RC-77 T/E cells, while integrin beta-1, integrin alpha-6, caveolin-1, laminin subunit gamma-2, and CD44 antigen were downregulated. The increased protein level of beta-catenin and the reduction of caveolin-1 protein level in the tumorigenic RC-77 T/E cells mirrored the upregulation of beta-catenin mRNA and downregulation of caveolin-1 mRNA in African-American prostate cancer specimens compared to non-malignant controls. After subtracting race-specific non-malignant RNA expression, beta-catenin and caveolin-1 mRNA expression levels were higher in African-American prostate cancer specimens than in Caucasian-American specimens. The “ECM-Receptor Interaction” and “Cell Adhesion Molecules”, and the “Tight Junction” and “Adherens Junction” pathways contained proteins are associated with RC-77 N/E and RC-77 T/E cells, respectively. Conclusions Our results suggest RC-77 T/E and RC-77 N/E cell lines can be distinguished by differentially expressed structural and cytoskeletal proteins, which appeared in several pathways across multiple analyses. Our results indicate that the expression of beta-catenin and caveolin-1 may be prostate cancer- and race-specific. Although the RC-77 cell model may not be representative of all African-American prostate cancer due to tumor heterogeneity, it is a unique resource for studying prostate cancer initiation and progression. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3462-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer S Myers
- Department of Chemistry and Biochemistry and Institute of Molecular Biophysics, Florida State University, 95 Chieftan Way, Tallahassee, FL, 32306-4390, USA
| | - Karin A Vallega
- Department of Chemistry and Biochemistry and Institute of Molecular Biophysics, Florida State University, 95 Chieftan Way, Tallahassee, FL, 32306-4390, USA
| | - Jason White
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL, 36088, USA
| | - Kaixian Yu
- Department of Biostatistics - Unit 1411, University of Texas MD Anderson Cancer Center, Houston, TX, 77030-1402, USA
| | - Clayton C Yates
- Department of Biology and Center for Cancer Research, Tuskegee University, Tuskegee, AL, 36088, USA
| | - Qing-Xiang Amy Sang
- Department of Chemistry and Biochemistry and Institute of Molecular Biophysics, Florida State University, 95 Chieftan Way, Tallahassee, FL, 32306-4390, USA.
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Appe AJ, Aggerholm A, Hansen MC, Ebbesen LH, Hokland P, Bentzen HHN, Nyvold CG. Differential expression levels and methylation status of ROBO1 in mantle cell lymphoma and chronic lymphocytic leukaemia. Int J Lab Hematol 2017; 39:e70-e73. [PMID: 28004534 DOI: 10.1111/ijlh.12615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
MESH Headings
- DNA Methylation
- DNA, Neoplasm/metabolism
- Female
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphoma, Mantle-Cell/metabolism
- Lymphoma, Mantle-Cell/pathology
- Male
- Neoplasm Proteins/biosynthesis
- Nerve Tissue Proteins/biosynthesis
- Receptors, Immunologic/biosynthesis
- Roundabout Proteins
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Affiliation(s)
- A J Appe
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - A Aggerholm
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - M C Hansen
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - L H Ebbesen
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - P Hokland
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - H H N Bentzen
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - C G Nyvold
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
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Lin HY, Cheng CH, Chen DT, Chen YA, Park JY. Coexpression and expression quantitative trait loci analyses of the angiogenesis gene-gene interaction network in prostate cancer. Transl Cancer Res 2016; 5:S951-S963. [PMID: 28664150 DOI: 10.21037/tcr.2016.10.55] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Prostate cancer (PCa) shows a substantial clinical heterogeneity. The existing risk classification for PCa prognosis based on clinical factors is not sufficient. Although some biomarkers for PCa aggressiveness have been identified, their underlying functional mechanisms are still unclear. We previously reported a gene-gene interaction network associated with PCa aggressiveness based on single nucleotide polymorphism (SNP)-SNP interactions in the angiogenesis pathway. The goal of this study is to investigate potential functional evidence of the involvement of the genes in this gene-gene interaction network. METHODS A total of 11 angiogenesis genes were evaluated. The crosstalks among genes were examined through coexpression and expression quantitative trait loci (eQTL) analyses. The study population is 352 Caucasian PCa patients in the Cancer Genome Atlas (TCGA) study. The pairwise coexpressions among the genes of interest were evaluated using the Spearman coefficient. The eQTL analyses were tested using the Kruskal-Wallis test. RESULTS Among all within gene and 55 possible pairwise gene evaluations, 12 gene pairs and one gene (MMP16) showed strong coexpression or significant eQTL evidence. There are nine gene pairs with a strong correlation (Spearman correlation ≥0.6, P<1×10-13). The top coexpressed gene pairs are EGFR-SP1 (r=0.73), ITGB3-HSPG2 (r=0.71), ITGB3-CSF1 (r=0.70), MMP16-FBLN5 (r=0.68), ITGB3-MMP16 (r=0.65), ITGB3-ROBO1 (r=0.62), CSF1-HSPG2 (r=0.61), CSF1-FBLN5 (r=0.6), and CSF1-ROBO1 (r=0.60). One cis-eQTL in MMP16 and five trans-eQTLs (MMP16-ESR1, ESR1-ROBO1, CSF1-ROBO1, HSPG2-ROBO1, and FBLN5-CSF1) are significant with a false discovery rate q value less than 0.2. CONCLUSIONS These findings provide potential biological evidence for the gene-gene interactions in this angiogenesis network. These identified interactions between the angiogenesis genes not only provide information for PCa etiology mechanism but also may serve as integrated biomarkers for building a risk prediction model for PCa aggressiveness.
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Affiliation(s)
- Hui-Yi Lin
- Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Chia-Ho Cheng
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Dung-Tsa Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Y Ann Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Jong Y Park
- Department of Cancer Epidemiology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
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30
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Villacis RAR, Abreu FB, Miranda PM, Domingues MAC, Carraro DM, Santos EMM, Andrade VP, Rossi BM, Achatz MI, Rogatto SR. ROBO1 deletion as a novel germline alteration in breast and colorectal cancer patients. Tumour Biol 2016; 37:3145-53. [PMID: 26427657 DOI: 10.1007/s13277-015-4145-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/23/2015] [Indexed: 01/22/2023] Open
Abstract
Despite one third of breast (BC) and colorectal cancer (CRC) cases having a hereditary component, only a small proportion can be explained by germline mutations. The aim of this study was to identify potential genomic alterations related to cancer predisposition. Copy number variations (CNVs) were interrogated in 113 unrelated cases fulfilling the criteria for hereditary BC/CRC and presenting non-pathogenic mutations in BRCA1, BRCA2, MLH1, MSH2, TP53, and CHEK2 genes. An identical germline deep intronic deletion of ROBO1 was identified in three index patients using two microarray platforms (Agilent 4x180K and Affymetrix CytoScan HD). The ROBO1 deletion was confirmed by quantitative PCR (qPCR). Six relatives were also evaluated by CytoScan HD Array. Genomic analysis confirmed a co-segregation of the ROBO1 deletion with the occurrence of cancer in two families. Direct sequencing revealed no pathogenic ROBO1 point mutations. Transcriptomic analysis (HTA 2.0, Affymetrix) in two breast carcinomas from a single patient revealed ROBO1 down-expression with no splicing events near the intronic deletion. Deeper in silico analysis showed several enhancer regions and a histone methylation mark in the deleted region. The ROBO1 deletion in a putative transcriptional regulatory region, its down-expression in tumor samples, and the results of the co-segregation analysis revealing the presence of the alteration in affected individuals suggest a pathogenic effect of the ROBO1 in cancer predisposition.
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Affiliation(s)
- Rolando A R Villacis
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil
| | - Francine B Abreu
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil
| | - Priscila M Miranda
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil
| | - Maria A C Domingues
- Department of Pathology, Faculty of Medicine, University of São Paulo State (UNESP), Botucatu, SP, Brazil
| | - Dirce M Carraro
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil
| | | | - Victor P Andrade
- Department of Pathology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | | | - Maria I Achatz
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Silvia R Rogatto
- International Research Center (CIPE), A.C. Camargo Cancer Center, Rua Taguá 440, São Paulo, CEP: 01508-010, SP, Brazil.
- Department of Urology, Faculty of Medicine, University of São Paulo State (UNESP), CEP: 18618-970, Botucatu, SP, Brazil.
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31
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He F, Zuo L. Redox Roles of Reactive Oxygen Species in Cardiovascular Diseases. Int J Mol Sci 2015; 16:27770-80. [PMID: 26610475 PMCID: PMC4661917 DOI: 10.3390/ijms161126059] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/06/2015] [Accepted: 11/11/2015] [Indexed: 02/07/2023] Open
Abstract
Cardiovascular disease (CVD), a major cause of mortality in the world, has been extensively studied over the past decade. However, the exact mechanism underlying its pathogenesis has not been fully elucidated. Reactive oxygen species (ROS) play a pivotal role in the progression of CVD. Particularly, ROS are commonly engaged in developing typical characteristics of atherosclerosis, one of the dominant CVDs. This review will discuss the involvement of ROS in atherosclerosis, specifically their effect on inflammation, disturbed blood flow and arterial wall remodeling. Pharmacological interventions target ROS in order to alleviate oxidative stress and CVD symptoms, yet results are varied due to the paradoxical role of ROS in CVD. Lack of effectiveness in clinical trials suggests that understanding the exact role of ROS in the pathophysiology of CVD and developing novel treatments, such as antioxidant gene therapy and nanotechnology-related antioxidant delivery, could provide a therapeutic advance in treating CVDs. While genetic therapies focusing on specific antioxidant expression seem promising in CVD treatments, multiple technological challenges exist precluding its immediate clinical applications.
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Affiliation(s)
- Feng He
- Department of Kinesiology, California State University-Chico, Chico, CA 95929, USA.
| | - Li Zuo
- Molecular Physiology and Rehabilitation Research Lab, Radiologic Sciences and Respiratory Therapy Division, School of Health and Rehabilitation Sciences, the Ohio State University College of Medicine, Columbus, OH 43210, USA.
- Interdisciplinary Biophysics Graduate Program, the Ohio State University, Columbus, OH 43210, USA.
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32
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Yang M, Liu R, Li X, Liao J, Pu Y, Pan E, Wang Y, Yin L. Epigenetic Repression of miR-218 Promotes Esophageal Carcinogenesis by Targeting ROBO1. Int J Mol Sci 2015; 16:27781-95. [PMID: 26610476 PMCID: PMC4661920 DOI: 10.3390/ijms161126062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/11/2015] [Accepted: 11/12/2015] [Indexed: 12/17/2022] Open
Abstract
miR-218, consisting of miR-218-1 at 4p15.31 and miR-218-2 at 5q35.1, was significantly decreased in esophageal squamous cell carcinoma (ESCC) in our previous study. The aim of this study was to determine whether aberrant methylation is associated with miR-218 repression. Bisulfite sequencing analysis (BSP), methylation specific PCR (MSP), and 5-aza-2'-deoxycytidine treatment assay were applied to determine the methyaltion status of miR-218 in cells and clinical samples. In vitro assays were performed to explore the role of miR-218. Results showed that miR-218-1 was significantly CpG hypermethylated in tumor tissues (81%, 34/42) compared with paired non-tumor tissues (33%, 14/42) (p < 0.05). However, no statistical difference was found in miR-218-2. Accordingly, expression of miR-218 was negatively correlated with miR-218-1 methylation status (p < 0.05). After demethylation treatment by 5-aza-2'-deoxycytidine, there was a 2.53- and 2.40-fold increase of miR-218 expression in EC109 and EC9706, respectively. miR-218 suppressed cell proliferation and arrested cells at G1 phase by targeting 3' untranslated region (3'UTR) of roundabout guidance receptor 1 (ROBO1). A negative correlation was found between miR-218 and ROBO1 mRNA expression in clinical samples. In conclusion, our results support that aberrant CpG hypermethylation at least partly accounts for miR-218 silencing in ESCC, which impairs its tumor-suppressive function.
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Affiliation(s)
- Miao Yang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Xiajun Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Juan Liao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
| | - Enchun Pan
- Huaian Center for Disease Control and Prevention, Huaian 223001, China.
| | - Yi Wang
- Huaian Center for Disease Control and Prevention, Huaian 223001, China.
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.
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33
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Ao JY, Chai ZT, Zhang YY, Zhu XD, Kong LQ, Zhang N, Ye BG, Cai H, Gao DM, Sun HC. Robo1 promotes angiogenesis in hepatocellular carcinoma through the Rho family of guanosine triphosphatases' signaling pathway. Tumour Biol 2015; 36:8413-24. [PMID: 26022159 DOI: 10.1007/s13277-015-3601-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/20/2015] [Indexed: 02/05/2023] Open
Abstract
Robo1 is a member of the Robo immunoglobulin superfamily of proteins, and it plays an important role in angiogenesis and cancer. In this study, we investigate the role of roundabout 1 (Robo1) in tumor angiogenesis in hepatocellular carcinoma (HCC). Firstly, the relationship between Robo1 expression on tumors and patient's survival and endothelial cells in tumor blood vessels and patient's survival was studied. Secondly, Robo1 was overexpressed or knocked down in human umbilical vein endothelial cells (HUVECs). Cell proliferation, motility, and tube formation were compared in HUVEC with different Robo1 expression. Also, HUVECs with different Robo1 expression were mixed with HCCLM3 and HepG2 hepatoma cells and then implanted in a nude mouse model to examine the effects of Robo1 in endothelial cells on tumor growth and angiogenesis. Cell motility-related molecules were studied to investigate the potential mechanism how Robo1 promoted tumor angiogenesis in HCC. The disease-free survival of the patients with high Robo1 expression in tumoral endothelial cells was significantly shorter than that of those with low expression (P = 0.021). Overexpression of Robo1 in HUVECs resulted in increased proliferation, motility, and tube formation in vitro. In the implanted mixture of tumor cells and HUVECs with an increased Robo1 expression, tumor growth and microvessel density were enhanced compared with controls. Robo1 promoted cell division cycle 42 (Cdc42) expression in HUVECs, and a distorted actin cytoskeleton in HUVECs was observed when Robo1 expression was suppressed. In conclusion, Robo1 promoted angiogenesis in HCC mediated by Cdc42.
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Affiliation(s)
- Jian-Yang Ao
- Liver Cancer Institute and Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Zong-Tao Chai
- Liver Cancer Institute and Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
- Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Yuan-Yuan Zhang
- Liver Cancer Institute and Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Xiao-Dong Zhu
- Liver Cancer Institute and Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Ling-Qun Kong
- Department of Hepatobiliary Surgery, Binzhou Medical College Affiliated Hospital, Binzhou, Shandong, 256610, China
| | - Ning Zhang
- Liver Cancer Institute and Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Bo-Gen Ye
- Liver Cancer Institute and Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Hao Cai
- Liver Cancer Institute and Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Dong-mei Gao
- Liver Cancer Institute and Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China
| | - Hui-Chuan Sun
- Liver Cancer Institute and Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, China.
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34
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Mathelier A, Lefebvre C, Zhang AW, Arenillas DJ, Ding J, Wasserman WW, Shah SP. Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas. Genome Biol 2015; 16:84. [PMID: 25903198 PMCID: PMC4467049 DOI: 10.1186/s13059-015-0648-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/07/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND With the rapid increase of whole-genome sequencing of human cancers, an important opportunity to analyze and characterize somatic mutations lying within cis-regulatory regions has emerged. A focus on protein-coding regions to identify nonsense or missense mutations disruptive to protein structure and/or function has led to important insights; however, the impact on gene expression of mutations lying within cis-regulatory regions remains under-explored. We analyzed somatic mutations from 84 matched tumor-normal whole genomes from B-cell lymphomas with accompanying gene expression measurements to elucidate the extent to which these cancers are disrupted by cis-regulatory mutations. RESULTS We characterize mutations overlapping a high quality set of well-annotated transcription factor binding sites (TFBSs), covering a similar portion of the genome as protein-coding exons. Our results indicate that cis-regulatory mutations overlapping predicted TFBSs are enriched in promoter regions of genes involved in apoptosis or growth/proliferation. By integrating gene expression data with mutation data, our computational approach culminates with identification of cis-regulatory mutations most likely to participate in dysregulation of the gene expression program. The impact can be measured along with protein-coding mutations to highlight key mutations disrupting gene expression and pathways in cancer. CONCLUSIONS Our study yields specific genes with disrupted expression triggered by genomic mutations in either the coding or the regulatory space. It implies that mutated regulatory components of the genome contribute substantially to cancer pathways. Our analyses demonstrate that identifying genomically altered cis-regulatory elements coupled with analysis of gene expression data will augment biological interpretation of mutational landscapes of cancers.
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Affiliation(s)
- Anthony Mathelier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, V5Z 4H4, Vancouver, BC, Canada.
| | - Calvin Lefebvre
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, V5Z 1L3, BC, Canada. .,Bioinformatics Graduate Program, University of British Columbia, Vancouver, V5Z 1L3, BC, Canada.
| | - Allen W Zhang
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, V5Z 4H4, Vancouver, BC, Canada. .,Bioinformatics Graduate Program, University of British Columbia, Vancouver, V5Z 1L3, BC, Canada.
| | - David J Arenillas
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, V5Z 4H4, Vancouver, BC, Canada.
| | - Jiarui Ding
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, V5Z 1L3, BC, Canada. .,Department of Computer Science, University of British Columbia, Vancouver, V6T 1Z4, BC, Canada.
| | - Wyeth W Wasserman
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, V5Z 4H4, Vancouver, BC, Canada.
| | - Sohrab P Shah
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, V5Z 1L3, BC, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, G227-2211, BC, Canada.
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