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Wu H, Geng Q, Shi W, Qiu C. Comprehensive pan-cancer analysis reveals CCDC58 as a carcinogenic factor related to immune infiltration. Apoptosis 2024; 29:536-555. [PMID: 38066393 DOI: 10.1007/s10495-023-01919-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2023] [Indexed: 02/18/2024]
Abstract
CCDC58, a member of the CCDC protein family, has been primarily associated with the malignant progression of hepatocellular carcinoma (HCC) and breast cancer, with limited research conducted on its involvement in other tumor types. We aimed to assess the significance of CCDC58 in pan-cancer. We utilized the TCGA, GTEx, and UALCAN databases to perform the differential expression of CCDC58 at both mRNA and protein levels. Prognostic value was evaluated through univariate Cox regression and Kaplan-Meier methods. Mutation and methylation analyses were conducted using the cBioPortal and SMART databases. We identified genes interacting with and correlated to CCDC58 through STRING and GEPIA2, respectively. Subsequently, we performed GO and KEGG enrichment analyses. To gain insights into the functional status of CCDC58 at the single-cell level, we utilized CancerSEA. We explored the correlation between CCDC58 and immune infiltration as well as immunotherapy using the ESTIMATE package, TIMER2.0, TISIDB, TIDE, TIMSO, and TCIA. We examined the relationship between CCDC58 and tumor heterogeneity, stemness, DNA methyltransferases, and MMR genes. Lastly, we constructed a nomogram based on CCDC58 in HCC and investigated its association with drug sensitivity. CCDC58 expression was significantly upregulated and correlated with poor prognosis across various tumor types. The mutation frequency of CCDC58 was found to be increased in 25 tumors. We observed a negative correlation between CCDC58 expression and the methylation sites in the majority of tumors. CCDC58 showed negative correlations with immune and stromal scores, as well as with NK T cells, Tregs, CAFs, endothelial cells, and immunomodulators. Its value in immunotherapy was comparable to that of tumor mutational burden. CCDC58 exhibited positive correlations with tumor heterogeneity, stemness, DNA methyltransferase genes, and MMR genes. In HCC, CCDC58 was identified as an independent risk factor and demonstrated potential associations with multiple drugs. CCDC58 demonstrates significant clinical value as a prognostic marker and indicator of immune response across various tumor types. Its comprehensive analysis provides insights into its potential implications in pan-cancer research.
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Affiliation(s)
- Huili Wu
- Department of Endodontics, Zhonglou Hospital, Changzhou Hospital of Traditional Chinese Medicine, Changzhou, China
| | - Qing Geng
- School of Exercise and Health, Shanghai University of Sport, Shanghai, China
| | - Wenxiang Shi
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Chenjie Qiu
- Department of General Surgery, Changzhou Hospital of Traditional Chinese Medicine, Changzhou, China.
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Miao Z, Cao Q, Liao R, Chen X, Li X, Bai L, Ma C, Deng X, Dai Z, Li J, Dong C. Elevated transcription and glycosylation of B3GNT5 promotes breast cancer aggressiveness. J Exp Clin Cancer Res 2022; 41:169. [PMID: 35526049 PMCID: PMC9077843 DOI: 10.1186/s13046-022-02375-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/27/2022] [Indexed: 12/12/2022] Open
Abstract
Background Basal-like breast cancer (BLBC) is the most aggressive subtype of breast cancer because of its aggressive biological characteristics and no effective targeted agents. However, the mechanism underlying its aggressive behavior remain poorly understood. β1,3-N-acetylglucosaminyltransferase V (B3GNT5) overexpression occurs specifically in BLBC. Here, we studied the possible molecular mechanisms of B3GBT5 promoting the aggressiveness of BLBC. Methods The potential effects of B3GNT5 on breast cancer cells were tested by colony formation, mammosphere formation, cell proliferation assay, flow cytometry and Western blotting. The glycosylation patterns of B3GNT5 and associated functions were determined by Western blotting, quantitative real-time PCR and flow cytometry. The effect of B3GNT5 expression on BLBC was assessed by in vitro and in vivo tumorigenesis model. Results In this study, we showed that B3GNT5 copy number amplification and hypomethylation of B3GNT5 promoter contributed to the overexpression of B3GNT5 in BLBC. Knockout of B3GNT5 strongly reduced surface expression of SSEA-1 and impeded cancer stem cell (CSC)-like properties of BLBC cells. Our results also showed that B3GNT5 protein was heavily N-glycosylated, which is critical for its protein stabilization. Clinically, elevated expression of B3GNT5 was correlated with high grade, large tumor size and poor survival, indicating poor prognosis of breast cancer patients. Conclusions Our work uncovers the critical association of B3GNT5 overexpression and glycosylation with enhanced CSCs properties in BLBC. These findings suggest that B3GNT5 has the potential to become a prognostic marker and therapeutic target for BLBC. Supplementary information The online version contains supplementary material available at 10.1186/s13046-022-02375-5.
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Gao S, Shi P, Tian Z, Yang X, Liu N. Overexpression of miR-1225 promotes the progression of breast cancer, resulting in poor prognosis. Clin Exp Med 2021; 21:287-296. [PMID: 33423149 DOI: 10.1007/s10238-020-00676-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/21/2020] [Indexed: 11/26/2022]
Abstract
Breast cancer is the most common cancer among women, with metastasis as the principal cause of mortality. MiR-1225 has been reported to play roles in the progression of various cancers, but its role in breast cancer was unclear. The expression of miR-1225 was investigated in breast cancer tissues and cells by quantitative real-time PCR. The role of miR-1225 in the cell process of OS was analyzed by CCK-8 assay and Transwell assay. The prognostic value of miR-1225 was evaluated by Kaplan-Meier survival curves and Cox regression analysis. miR-1225 was significantly upregulated in breast cancer tissues, which was associated with the TNM stage of breast cancer patients. The prognosis of patients with high miR-1225 expression was worse than that of patients with low miR-1225 expression, which indicated that miR-1225 acted as an independent factor for the prognosis of breast cancer. Additionally, the upregulation of miR-1225 promoted cell proliferation, migration, and invasion of breast cancer, which suggested miR-1225 might be involved in the progression of breast cancer. JAK1 was identified as the direct target of miR-1225, which was also involved in cell proliferation, migration, and invasion of breast cancer. The overexpression of miR-1225 in breast cancer indicates a poor prognosis of patients and promotes the progression of breast cancer by targeting JAK1. miR-1225 may be a biomarker and therapeutic target for the treatment of breast cancer.
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Affiliation(s)
- Shangfa Gao
- Department of General Surgery, Chengwu People's Hospital Affiliated to Shandong First Medical University, Heze, 274200, Shandong, China
| | - Peng Shi
- Department of Gland Surgery, Shandong Provincial Hospital, Jinan, 250021, Shandong, China
| | - Zhishuai Tian
- Department of General Surgery, Chengwu People's Hospital Affiliated to Shandong First Medical University, Heze, 274200, Shandong, China
| | - Xingwang Yang
- Department of General Surgery, Zibo City Linzi District People's Hospital, No. 139, Huangong Road, Zibo, 255400, Shandong, China.
| | - Ning Liu
- Department of Breast Surgery, China-Japan Union Hospital of Jilin University, No. 126 Xi'antai Avenue, Changchun City, 130033, Jilin Province, China.
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Harnan S, Tappenden P, Cooper K, Stevens J, Bessey A, Rafia R, Ward S, Wong R, Stein RC, Brown J. Tumour profiling tests to guide adjuvant chemotherapy decisions in early breast cancer: a systematic review and economic analysis. Health Technol Assess 2020; 23:1-328. [PMID: 31264581 DOI: 10.3310/hta23300] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Breast cancer and its treatment can have an impact on health-related quality of life and survival. Tumour profiling tests aim to identify whether or not women need chemotherapy owing to their risk of relapse. OBJECTIVES To conduct a systematic review of the effectiveness and cost-effectiveness of the tumour profiling tests oncotype DX® (Genomic Health, Inc., Redwood City, CA, USA), MammaPrint® (Agendia, Inc., Amsterdam, the Netherlands), Prosigna® (NanoString Technologies, Inc., Seattle, WA, USA), EndoPredict® (Myriad Genetics Ltd, London, UK) and immunohistochemistry 4 (IHC4). To develop a health economic model to assess the cost-effectiveness of these tests compared with clinical tools to guide the use of adjuvant chemotherapy in early-stage breast cancer from the perspective of the NHS and Personal Social Services. DESIGN A systematic review and health economic analysis were conducted. REVIEW METHODS The systematic review was partially an update of a 2013 review. Nine databases were searched in February 2017. The review included studies assessing clinical effectiveness in people with oestrogen receptor-positive, human epidermal growth factor receptor 2-negative, stage I or II cancer with zero to three positive lymph nodes. The economic analysis included a review of existing analyses and the development of a de novo model. RESULTS A total of 153 studies were identified. Only one completed randomised controlled trial (RCT) using a tumour profiling test in clinical practice was identified: Microarray In Node-negative Disease may Avoid ChemoTherapy (MINDACT) for MammaPrint. Other studies suggest that all the tests can provide information on the risk of relapse; however, results were more varied in lymph node-positive (LN+) patients than in lymph node-negative (LN0) patients. There is limited and varying evidence that oncotype DX and MammaPrint can predict benefit from chemotherapy. The net change in the percentage of patients with a chemotherapy recommendation or decision pre/post test ranged from an increase of 1% to a decrease of 23% among UK studies and a decrease of 0% to 64% across European studies. The health economic analysis suggests that the incremental cost-effectiveness ratios for the tests versus current practice are broadly favourable for the following scenarios: (1) oncotype DX, for the LN0 subgroup with a Nottingham Prognostic Index (NPI) of > 3.4 and the one to three positive lymph nodes (LN1-3) subgroup (if a predictive benefit is assumed); (2) IHC4 plus clinical factors (IHC4+C), for all patient subgroups; (3) Prosigna, for the LN0 subgroup with a NPI of > 3.4 and the LN1-3 subgroup; (4) EndoPredict Clinical, for the LN1-3 subgroup only; and (5) MammaPrint, for no subgroups. LIMITATIONS There was only one completed RCT using a tumour profiling test in clinical practice. Except for oncotype DX in the LN0 group with a NPI score of > 3.4 (clinical intermediate risk), evidence surrounding pre- and post-test chemotherapy probabilities is subject to considerable uncertainty. There is uncertainty regarding whether or not oncotype DX and MammaPrint are predictive of chemotherapy benefit. The MammaPrint analysis uses a different data source to the other four tests. The Translational substudy of the Arimidex, Tamoxifen, Alone or in Combination (TransATAC) study (used in the economic modelling) has a number of limitations. CONCLUSIONS The review suggests that all the tests can provide prognostic information on the risk of relapse; results were more varied in LN+ patients than in LN0 patients. There is limited and varying evidence that oncotype DX and MammaPrint are predictive of chemotherapy benefit. Health economic analyses indicate that some tests may have a favourable cost-effectiveness profile for certain patient subgroups; all estimates are subject to uncertainty. More evidence is needed on the prediction of chemotherapy benefit, long-term impacts and changes in UK pre-/post-chemotherapy decisions. STUDY REGISTRATION This study is registered as PROSPERO CRD42017059561. FUNDING The National Institute for Health Research Health Technology Assessment programme.
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Affiliation(s)
- Sue Harnan
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Paul Tappenden
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Katy Cooper
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - John Stevens
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Alice Bessey
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Rachid Rafia
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Sue Ward
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Ruth Wong
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Robert C Stein
- University College London Hospitals Biomedical Research Centre, London, UK.,Research Department of Oncology, University College London, London, UK
| | - Janet Brown
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
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Huang R, Guo J, Yan P, Zhai S, Hu P, Zhu X, Zhang J, Qiao Y, Zhang Y, Liu H, Huang L, Zhang J, Yang D, Huang Z. The Construction of Bone Metastasis-Specific Prognostic Model and Co-expressed Network of Alternative Splicing in Breast Cancer. Front Cell Dev Biol 2020; 8:790. [PMID: 32984314 PMCID: PMC7477087 DOI: 10.3389/fcell.2020.00790] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/28/2020] [Indexed: 01/17/2023] Open
Abstract
Background Breast cancer (BRCA) ranks among the top most common female malignancies and was regarded as incurable when combined with bone and distant metastasis. Alternative splicing events (ASEs) together with splicing factors (SFs) were considered responsible for the development and progression of tumors. Methods Datasets including RNA sequencing and ASEs of BRCA samples were achieved from TCGA and TCGASpliceSeq databases. Then, a survival model was built including 15 overall-survival-associated splicing events (OS-SEs) by Cox regression and Lasso regression. The co-expressed SFs of each bone-and-distant-metastasis-related OS-SE were discovered by Pearson correlation analysis. Additionally, Gene Set Variation Analysis (GSVA) was performed to identify the downstream mechanisms of the key OS-SEs. Finally, the results were validated in different online platforms. Results A reliable survival model was established (the area under ROC = 0.856), and CIRBP was found co-expressed with FAM110B (R = 0.320, P < 0.001) associated with the fatty acid metabolism pathway. Conclusion Aberrant SF, CIRBP, regulated a specific ASE, exon skip (ES) of FAM110B, during which the fatty acid metabolism pathway played an essential part in tumorigenesis and prognosis of BRCA.
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Affiliation(s)
- Runzhi Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai, China.,Tongji University School of Medicine, Shanghai, China
| | - Juanru Guo
- Tongji University School of Mathematical Sciences, Tongji University, Shanghai, China
| | - Penghui Yan
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Suna Zhai
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Peng Hu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaolong Zhu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiayao Zhang
- Tongji University School of Mathematical Sciences, Tongji University, Shanghai, China
| | - Yannan Qiao
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Zhang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hui Liu
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ling Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Zhang
- Tongji University School of Medicine, Shanghai, China
| | - Daoke Yang
- Department of Radiotherapy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zongqiang Huang
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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6
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TSPAN8 promotes cancer cell stemness via activation of sonic Hedgehog signaling. Nat Commun 2019; 10:2863. [PMID: 31253779 PMCID: PMC6599078 DOI: 10.1038/s41467-019-10739-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 05/21/2019] [Indexed: 01/02/2023] Open
Abstract
Cancer stem cells (CSCs) represent a major source of treatment resistance and tumor progression. However, regulation of CSCs stemness is not entirely understood. Here, we report that TSPAN8 expression is upregulated in breast CSCs, promotes the expression of the stemness gene NANOG, OCT4, and ALDHA1, and correlates with therapeutic resistance. Mechanistically, TSPAN8 interacts with PTCH1 and inhibits the degradation of the SHH/PTCH1 complex through recruitment of deubiquitinating enzyme ATXN3. This results in the translocation of SMO to cilia, downstream gene expression, resistance of CSCs to chemotherapeutic agents, and enhances tumor formation in mice. Accordingly, expression levels of TSPAN8, PTCH1, SHH, and ATXN3 are positively correlated in human breast cancer specimens, and high TSPAN8 and ATXN3 expression levels correlate with poor prognosis. These findings reveal a molecular basis of TSPAN8-enhanced Sonic Hedgehog signaling and highlight a role for TSPAN8 in promoting cancer stemness. Tetraspanin 8 (TSPAN8) has been implicated in a number of different tumours, but the underlying mechanisms remain unclear. Here, in breast cancer the authors highlight a role for TSPAN8 in promoting tumorigenesis through the activation of Hedgehog signalling.
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7
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Saygin C, Matei D, Majeti R, Reizes O, Lathia JD. Targeting Cancer Stemness in the Clinic: From Hype to Hope. Cell Stem Cell 2018; 24:25-40. [PMID: 30595497 DOI: 10.1016/j.stem.2018.11.017] [Citation(s) in RCA: 320] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tumors are composed of non-homogeneous cell populations exhibiting varying degrees of genetic and functional heterogeneity. Cancer stem cells (CSCs) are capable of sustaining tumors by manipulating genetic and non-genetic factors to metastasize, resist treatment, and maintain the tumor microenvironment. Understanding the key traits and mechanisms of CSC survival provides opportunities to improve patient outcomes via improved prognostic models and therapeutics. Here, we review the clinical significance of CSCs and results of potential CSC-targeting therapies in various cancers. We discuss barriers to translating cues from pre-clinical models into clinical applications and propose new strategies for rational design of future anti-CSC trials.
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Affiliation(s)
- Caner Saygin
- Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Daniela Matei
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ravindra Majeti
- Division of Hematology, Department of Medicine, Cancer Institute and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ofer Reizes
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44192, USA
| | - Justin D Lathia
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH 44192, USA.
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8
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Xi T, Zhang G. Integrated analysis of tumor differentiation genes in pancreatic adenocarcinoma. PLoS One 2018; 13:e0193427. [PMID: 29596435 PMCID: PMC5875763 DOI: 10.1371/journal.pone.0193427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 02/09/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Tumor differentiation is an important process in the development of cancer. It is valuable to identify key differentiation related genes in the prognosis and therapy of pancreatic adenocarcinoma. METHODS The mRNA expression data were downloaded from the Cancer Genome Atlas database. Then, differentially expressed tumor differentiation related genes were identified. Additionally, Gene Ontology functional categories and Kyoto Encyclopedia of Genes and Genomes biochemical pathway was used to explore the function. In addition, receiver operating characteristic and survival analysis were carried out to assess the diagnosis and prognosis value. Finally, the electronic validation of selected tumor differentiation related genes was performed. RESULTS A total of 932 genes were identified. Among which, 8 genes including JUB, ERLIN1, HMGA2, FAM110B, EGFR, MCM2, TCTA and SSTR1 were differentially expressed in all different tumor differentiation grades. Functional analysis revealed those genes between highly differentiated and other differentiation were remarkably enriched in pancreatic adenocarcinoma and cell cycle pathway. Finally, ERLIN1, HMGA2, FAM110B, EGFR, MCM2, BCL2L1, E2F1 and RAC1 were associated with the survival time of pancreatic adenocarcinoma patient. Among these genes, JUB, ERLIN1, FAM110B, MCM2 and BCL2L1 also had a diagnosis value for pancreatic adenocarcinoma. Additionally, the expression trend of JUB, HMGA2 and MCM2 was increased along with the tumor differentiation grades. And the expression trend of FAM110B was decreased along with the tumor differentiation grades. The electronic validation result was consistent with the bioinformatics analysis. CONCLUSIONS 12 tumor differentiation related genes including JUB, ERLIN1, HMGA2, FAM110B, EGFR, MCM2, TCTA, SSTR1, BCL2L1, E2F1, RAC1 and STAT1 played crucial roles in the differentiation of pancreatic adenocarcinoma.
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Affiliation(s)
- Ting Xi
- Department of Gastroenterology, First People’s Hospital of Liaocheng, Liaocheng, Shandong Province, China
- * E-mail:
| | - Guizhi Zhang
- Department of Gastroenterology, Second People’s Hospital of Liaocheng, Liaocheng, Shandong Province, China
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9
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Wang P, Shan L, Xue L, Zheng B, Ying J, Lu N. Genome wide copy number analyses of superficial esophageal squamous cell carcinoma with and without metastasis. Oncotarget 2018; 8:5069-5080. [PMID: 27974698 PMCID: PMC5354893 DOI: 10.18632/oncotarget.13847] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 11/21/2016] [Indexed: 01/08/2023] Open
Abstract
Superficial esophageal squamous cell carcinoma (ESCC) is generally considered a subtype of less invasive ESCC. Yet a subset of these superficial ESCC would have metastasis after esophagostomy or endoscopic resection and lead to poor prognosis. The objective of this study is to determine biomarkers that can identify such subset of superficial ESCC that would have metastasis after surgery using genome wide copy number alteration (CNA) analyses. The CNAs of 38 cases of superficial ESCCs originated from radical surgery, including 19 without metastasis and 19 with metastasis within 5 years’ post-surgery, were analyzed using Affymetrix OncoScan™ FFPE Assay. A 39-gene signature was identified which characterized the subset of superficial ESCC with high risk of metastasis after surgery. In addition, recurrent CNAs of superficial ESCC were also investigated in the study. Amplification of 11q13.3 (FGF4) and deletion of 9p21.3 (CDKN2A) were found to be recurrent in all 38 superficial ESCCs analyzed. Notably amplifications of 3p26.33 (SOX2OT), 8q24.21 (MYC), 14q21.1 (FOXA1) and deletion of 3p12.1 (GBE1) were only found to be recurrent in metastaic superficial ESCCs. In conclusion, using CNAs analyses, we identify a 39-gene signature which characterizes the high risk metastatic superficial ESCCs and discover several recurrent CNAs that might be the driver alterations in metastasis among superficial ESCCs.
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Affiliation(s)
- Pengjiao Wang
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Ling Shan
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Liyan Xue
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Bo Zheng
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Ning Lu
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
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Abstract
Acute leukemias are hematologic malignancies with aggressive behavior especially in adult population. With the introduction of new gene expression and sequencing technologies there have been advances in the knowledge of the genetic landscape of acute leukemias. A more detailed analysis allows for the identification of additional alterations in epigenetic regulators that have a profound impact in cellular biology without changes in DNA sequence. These epigenetic alterations disturb the physiological balance between gene activation and gene repression and contribute to aberrant gene expression, contributing significantly to the leukemic pathogenesis and maintenance. We review epigenetic changes in acute leukemia in relation to what is known about their mechanism of action, their prognostic role and their potential use as therapeutic targets, with important implications for precision medicine.
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11
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Sithara S, Crowley TM, Walder K, Aston-Mourney K. Gene expression signature: a powerful approach for drug discovery in diabetes. J Endocrinol 2017; 232:R131-R139. [PMID: 27927696 DOI: 10.1530/joe-16-0515] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 12/07/2016] [Indexed: 12/21/2022]
Abstract
Type 2 diabetes (T2D) is increasing in prevalence at an alarming rate around the world. Much effort has gone into the discovery and design of antidiabetic drugs; however, those already available are unable to combat the underlying causes of the disease and instead only moderate the symptoms. The reason for this is that T2D is a complex disease, and attempts to target one biological pathway are insufficient to combat the full extent of the disease. Additionally, the underlying pathophysiology of this disease is yet to be fully elucidated making it difficult to design drugs that target the mechanisms involved. Therefore, the approach of designing new drugs aimed at a specific molecular target is not optimal and a more expansive, unbiased approach is required. In this review, we will look at the current state of diabetes treatments and how these target the disease symptoms but are unable to combat the underlying causes. We will also review how the technique of gene expression signatures (GESs) has been used successfully for other complex diseases and how this may be applied as a powerful tool for the discovery of new drugs for T2D.
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Affiliation(s)
- Smithamol Sithara
- Metabolic Research UnitSchool of Medicine, Deakin University, Geelong, Australia
| | - Tamsyn M Crowley
- School of MedicineMMR, Bioinformatics Core Research Facility, Deakin University, Geelong, Australia
| | - Ken Walder
- Metabolic Research UnitSchool of Medicine, Deakin University, Geelong, Australia
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Girotra S, Yeghiazaryan K, Golubnitschaja O. Potential biomarker panels in overall breast cancer management: advancements by multilevel diagnostics. Per Med 2016; 13:469-484. [PMID: 29767597 DOI: 10.2217/pme-2016-0020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Breast cancer (BC) prevalence has reached an epidemic scale with half a million deaths annually. Current deficits in BC management include predictive and preventive approaches, optimized screening programs, individualized patient profiling, highly sensitive detection technologies for more precise diagnostics and therapy monitoring, individualized prediction and effective treatment of BC metastatic disease. To advance BC management, paradigm shift from delayed to predictive, preventive and personalized medical services is essential. Corresponding step forwards requires innovative multilevel diagnostics procuring specific panels of validated biomarkers. Here, we discuss current instrumental advancements including genomics, proteomics, epigenetics, miRNA, metabolomics, circulating tumor cells and cancer stem cells with a focus on biomarker discovery and multilevel diagnostic panels. A list of the recommended biomarker candidates is provided.
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Cruz-Rodriguez N, Combita AL, Enciso LJ, Quijano SM, Pinzon PL, Lozano OC, Castillo JS, Li L, Bareño J, Cardozo C, Solano J, Herrera MV, Cudris J, Zabaleta J. High expression of ID family and IGJ genes signature as predictor of low induction treatment response and worst survival in adult Hispanic patients with B-acute lymphoblastic leukemia. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2016; 35:64. [PMID: 27044543 PMCID: PMC4820984 DOI: 10.1186/s13046-016-0333-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 03/22/2016] [Indexed: 12/27/2022]
Abstract
Background B-Acute lymphoblastic leukemia (B-ALL) represents a hematologic malignancy with poor clinical outcome and low survival rates in adult patients. Remission rates in Hispanic population are almost 30 % lower and Overall Survival (OS) nearly two years inferior than those reported in other ethnic groups. Only 61 % of Colombian adult patients with ALL achieve complete remission (CR), median overall survival is 11.3 months and event-free survival (EFS) is 7.34 months. Identification of prognostic factors is crucial for the application of proper treatment strategies and subsequently for successful outcome. Our goal was to identify a gene expression signature that might correlate with response to therapy and evaluate the utility of these as prognostic tool in hispanic patients. Methods We included 43 adult patients newly diagnosed with B-ALL. We used microarray analysis in order to identify genes that distinguish poor from good response to treatment using differential gene expression analysis. The expression profile was validated by real-time PCR (RT-PCT). Results We identified 442 differentially expressed genes between responders and non-responders to induction treatment. Hierarchical analysis according to the expression of a 7-gene signature revealed 2 subsets of patients that differed in their clinical characteristics and outcome. Conclusions Our study suggests that response to induction treatment and clinical outcome of Hispanic patients can be predicted from the onset of the disease and that gene expression profiles can be used to stratify patient risk adequately and accurately. The present study represents the first that shows the gene expression profiling of B-ALL Colombian adults and its relevance for stratification in the early course of disease. Electronic supplementary material The online version of this article (doi:10.1186/s13046-016-0333-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nataly Cruz-Rodriguez
- Programa de Investigación e Innovación en Leucemias Agudas y Crónicas (PILAC), Instituto Nacional de Cancerología, Bogotá, Colombia.,Group of Investigation in Biology of Cancer, Instituto Nacional de Cancerología, Calle 1 # 9-85, Bogotá, Colombia.,Programa de Doctorado en Ciencias Biológicas, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Alba L Combita
- Programa de Investigación e Innovación en Leucemias Agudas y Crónicas (PILAC), Instituto Nacional de Cancerología, Bogotá, Colombia. .,Group of Investigation in Biology of Cancer, Instituto Nacional de Cancerología, Calle 1 # 9-85, Bogotá, Colombia. .,Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia.
| | - Leonardo J Enciso
- Programa de Investigación e Innovación en Leucemias Agudas y Crónicas (PILAC), Instituto Nacional de Cancerología, Bogotá, Colombia.,Grupo de Hemato Oncología, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Sandra M Quijano
- Grupo de Inmunobiología y Biología Celular, Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.,Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Paula L Pinzon
- Group of Investigation in Biology of Cancer, Instituto Nacional de Cancerología, Calle 1 # 9-85, Bogotá, Colombia
| | - Olga C Lozano
- Group of Investigation in Biology of Cancer, Instituto Nacional de Cancerología, Calle 1 # 9-85, Bogotá, Colombia
| | - Juan S Castillo
- Programa de Investigación e Innovación en Leucemias Agudas y Crónicas (PILAC), Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Li Li
- Stanley S. Scott Cancer Center, Center Louisiana State University Health Sciences Center Louisiana Cancer Research Center, 1700 Tulane Ave, Room 909, New Orleans, LA, USA
| | | | | | - Julio Solano
- Hospital Universitario San Ignacio, Bogotá, Colombia
| | | | | | - Jovanny Zabaleta
- Stanley S. Scott Cancer Center, Center Louisiana State University Health Sciences Center Louisiana Cancer Research Center, 1700 Tulane Ave, Room 909, New Orleans, LA, USA. .,Department of Pediatrics, Center Louisiana State University Health Sciences Center Louisiana Cancer Research Center, 1700 Tulane Ave, Room 909, New Orleans, LA, USA.
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14
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Carbognin L, Sperduti I, Brunelli M, Marcolini L, Nortilli R, Pilotto S, Zampiva I, Merler S, Fiorio E, Filippi E, Manfrin E, Pellini F, Bonetti F, Pollini GP, Tortora G, Bria E. Subpopulation Treatment Effect Pattern Plot (STEPP) analysis of Ki67 assay according to histology: prognostic relevance for resected early stage 'pure' and 'mixed' lobular breast cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2016; 35:50. [PMID: 27000271 PMCID: PMC4802900 DOI: 10.1186/s13046-016-0325-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/16/2016] [Indexed: 01/21/2023]
Abstract
Background The aim of this analysis was to investigate the potential impact of Ki67 assay in a series of patients affected by early stage invasive lobular carcinoma (ILC) undergone surgery. Methods Clinical-pathological data were correlated with disease-free and overall survival (DFS/OS). The maximally selected Log-Rank statistics analysis was applied to the Ki67 continuous variable to estimate appropriate cut-offs. The Subpopulation Treatment Effect Pattern Plot (STEPP) analysis was performed to assess the interaction between ‘pure’ or ‘mixed’ histology ILC and Ki67. Results At a median follow-up of 67 months, 10-years DFS and OS of 405 patients were 67.8 and 79.8 %, respectively. Standardized Log-Rank statistics identified 2 optimal cut-offs (6 and 21 %); 10-years DFS and OS were 75.1, 66.5, and 30.2 % (p = 0.01) and 84.3, 76.4 and 59 % (p = 0.003), for patients with a Ki67 < 6 %, between 6 and 21 %, and >21 %, respectively. Ki67 and lymph-node status were independent predictor for longer DFS and OS at the multivariate analysis, with radiotherapy (for DFS) and age (for OS). Ki67 highly replicated at the internal cross-validation analysis (DFS 85 %, OS 100 %). The STEPP analysis showed that DFS rate decreases as Ki67 increases and those patients with ‘pure’ ILC performed worse than ‘mixed’ histology. Conclusions Despite the retrospective and exploratory nature of the study, Ki67 was able to significantly discriminate the prognosis of patients with ILC, and the effect was more pronounced for patients with ‘pure’ ILC. Electronic supplementary material The online version of this article (doi:10.1186/s13046-016-0325-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luisa Carbognin
- Medical Oncology, University of Verona, Azienda Ospedaliera Universitaria Integrata, P.le L.A. Scuro 10, 37124, Verona, Italy
| | | | - Matteo Brunelli
- Department of Pathology and Diagnostic, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Lisa Marcolini
- Department of Pathology and Diagnostic, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Rolando Nortilli
- Medical Oncology, University of Verona, Azienda Ospedaliera Universitaria Integrata, P.le L.A. Scuro 10, 37124, Verona, Italy
| | - Sara Pilotto
- Medical Oncology, University of Verona, Azienda Ospedaliera Universitaria Integrata, P.le L.A. Scuro 10, 37124, Verona, Italy
| | - Ilaria Zampiva
- Medical Oncology, University of Verona, Azienda Ospedaliera Universitaria Integrata, P.le L.A. Scuro 10, 37124, Verona, Italy
| | - Sara Merler
- Medical Oncology, University of Verona, Azienda Ospedaliera Universitaria Integrata, P.le L.A. Scuro 10, 37124, Verona, Italy
| | - Elena Fiorio
- Medical Oncology, University of Verona, Azienda Ospedaliera Universitaria Integrata, P.le L.A. Scuro 10, 37124, Verona, Italy
| | - Elisa Filippi
- Medical Oncology, University of Verona, Azienda Ospedaliera Universitaria Integrata, P.le L.A. Scuro 10, 37124, Verona, Italy
| | - Erminia Manfrin
- Biostatistics, Regina Elena National Cancer Institute, Rome, Italy
| | - Francesca Pellini
- Chirurgia 'A', Department of Surgery and Oncology, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Franco Bonetti
- Biostatistics, Regina Elena National Cancer Institute, Rome, Italy
| | - Giovanni Paolo Pollini
- Department of Pathology and Diagnostic, University of Verona, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Giampaolo Tortora
- Medical Oncology, University of Verona, Azienda Ospedaliera Universitaria Integrata, P.le L.A. Scuro 10, 37124, Verona, Italy
| | - Emilio Bria
- Medical Oncology, University of Verona, Azienda Ospedaliera Universitaria Integrata, P.le L.A. Scuro 10, 37124, Verona, Italy.
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15
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Abstract
The cancer stem cell model in solid tumors has evolved significantly from the early paradigm shifting work highlighting parallels between the stem cell hierarchy in hematologic malignancies and solid tumors. Putative stem cells can dedifferentiated, be induced by context, and be the result of accumulated genetic mutations. The simple hypothesis that stem cell therapies will overcome the minority of cells that lead to recurrence has evolved with it. Nevertheless, the body of evidence that this field is clinically relevant in patients and patient care has grown with the complexity of the hypotheses, and numerous clinical strategies to target these cells have been identified. Herein we review this progress and highlight the work still outstanding.
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Affiliation(s)
- Wendy A Woodward
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Richard P Hill
- Princess Margaret Cancer Centre, Ontario Cancer Insitute, Toronto, ON, M5G 2M9, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
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16
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Shen Y, Wang Z, Loo LWM, Ni Y, Jia W, Fei P, Risch HA, Katsaros D, Yu H. LINC00472 expression is regulated by promoter methylation and associated with disease-free survival in patients with grade 2 breast cancer. Breast Cancer Res Treat 2015; 154:473-82. [PMID: 26564482 DOI: 10.1007/s10549-015-3632-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 11/03/2015] [Indexed: 01/06/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a class of newly recognized DNA transcripts that have diverse biological activities. Dysregulation of lncRNAs may be involved in many pathogenic processes including cancer. Recently, we found an intergenic lncRNA, LINC00472, whose expression was correlated with breast cancer progression and patient survival. Our findings were consistent across multiple clinical datasets and supported by results from in vitro experiments. To evaluate further the role of LINC00472 in breast cancer, we used various online databases to investigate possible mechanisms that might affect LINC00472 expression in breast cancer. We also analyzed associations of LINC00472 with estrogen receptor, tumor grade, and molecular subtypes in additional online datasets generated by microarray platforms different from the one we investigated previously. We found that LINC00472 expression in breast cancer was regulated more possibly by promoter methylation than by the alteration of gene copy number. Analysis of additional datasets confirmed our previous findings of high expression of LINC00472 associated with ER-positive and low-grade tumors and favorable molecular subtypes. Finally, in nine datasets, we examined the association of LINC00472 expression with disease-free survival in patients with grade 2 tumors. Meta-analysis of the datasets showed that LINC00472 expression in breast tumors predicted the recurrence of breast cancer in patients with grade 2 tumors. In summary, our analyses confirm that LINC00472 is functionally a tumor suppressor, and that assessing its expression in breast tumors may have clinical implications in breast cancer management.
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Affiliation(s)
- Yi Shen
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA
| | - Zhanwei Wang
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA
| | - Lenora W M Loo
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA
| | - Yan Ni
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA
| | - Wei Jia
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA
| | - Peiwen Fei
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | | | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, 701 Ilalo Street, Honolulu, HI, 96813, USA.
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17
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Wang Z, Katsaros D, Shen Y, Fu Y, Canuto EM, Benedetto C, Lu L, Chu WM, Risch HA, Yu H. Biological and Clinical Significance of MAD2L1 and BUB1, Genes Frequently Appearing in Expression Signatures for Breast Cancer Prognosis. PLoS One 2015; 10:e0136246. [PMID: 26287798 PMCID: PMC4546117 DOI: 10.1371/journal.pone.0136246] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 07/31/2015] [Indexed: 12/15/2022] Open
Abstract
To investigate the biologic relevance and clinical implication of genes involved in multiple gene expression signatures for breast cancer prognosis, we identified 16 published gene expression signatures, and selected two genes, MAD2L1 and BUB1. These genes appeared in 5 signatures and were involved in cell-cycle regulation. We analyzed the expression of these genes in relation to tumor features and disease outcomes. In vitro experiments were also performed in two breast cancer cell lines, MDA-MB-231 and MDA-MB-468, to assess cell proliferation, migration and invasion after knocking down the expression of these genes. High expression of these genes was found to be associated with aggressive tumors and poor disease-free survival of 203 breast cancer patients in our study, and the association with survival was confirmed in an online database consisting of 914 patients. In vitro experiments demonstrated that lowering the expression of these genes by siRNAs reduced tumor cell growth and inhibited cell migration and invasion. Our investigation suggests that MAD2L1 and BUB1 may play important roles in breast cancer progression, and measuring the expression of these genes may assist the prediction of breast cancer prognosis.
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Affiliation(s)
- Zhanwei Wang
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Dionyssios Katsaros
- Department of Surgical Sciences, Gynecologic Oncology, Azienda Ospedaliero-Universitaria Città della Salute, Turin, Italy
| | - Yi Shen
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Yuanyuan Fu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Emilie Marion Canuto
- Department of Surgical Sciences, Gynecologic Oncology, Azienda Ospedaliero-Universitaria Città della Salute, Turin, Italy
| | - Chiara Benedetto
- Department of Surgical Sciences, Gynecologic Oncology, Azienda Ospedaliero-Universitaria Città della Salute, Turin, Italy
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Wen-Ming Chu
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Harvey A. Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
- * E-mail:
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18
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Apostolou P, Toloudi M, Papasotiriou I. Identification of genes involved in breast cancer and breast cancer stem cells. BREAST CANCER-TARGETS AND THERAPY 2015. [PMID: 26203276 PMCID: PMC4507490 DOI: 10.2147/bctt.s85202] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Breast cancer is the most frequent type of cancer in women. Great progress has been made in its treatment but relapse is common. One hypothesis to account for the high recurrence rates is the presence of cancer stem cells (CSCs), which have the ability to self-renew and differentiate into multiple malignant cell types. This study aimed to determine genes that are expressed in breast cancer and breast CSCs and to investigate their correlation with stemness. RNA was extracted from established breast cancer cell lines and from CSCs derived from five different breast cancer patients. DNA microarray analysis was performed and any upregulated genes were also studied in other cancer types, including colorectal and lung cancer. For genes that were expressed only in breast cancer, knockdown-based experiments were performed. Finally, the gene expression levels of stemness transcription factors were measured. The outcome of the analysis indicated a group of genes that were aberrantly expressed mainly in breast cancer cells with stemness properties. Knockdown experiments confirmed the impact of several of these on NANOG, OCT3/4, and SOX2 transcription factors. It seems that several genes that are not directly related with hormone metabolism and basic signal transduction pathways might have an important role in relapse and disease progression and, thus, can be targeted for new treatment approaches for breast cancer.
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Affiliation(s)
- Panagiotis Apostolou
- Research and Development Department, Research Genetic Cancer Centre Ltd, Florina, Greece
| | - Maria Toloudi
- Research and Development Department, Research Genetic Cancer Centre Ltd, Florina, Greece
| | - Ioannis Papasotiriou
- Research and Development Department, Research Genetic Cancer Centre Ltd, Florina, Greece
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19
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A novel embryonic plasticity gene signature that predicts metastatic competence and clinical outcome. Sci Rep 2015; 5:11766. [PMID: 26123483 PMCID: PMC4485318 DOI: 10.1038/srep11766] [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: 01/05/2015] [Accepted: 06/02/2015] [Indexed: 12/16/2022] Open
Abstract
Currently, very few prognosticators accurately predict metastasis in cancer patients. In order to complete the metastatic cascade and successfully colonize distant sites, carcinoma cells undergo dynamic epithelial-mesenchymal-transition (EMT) and its reversal, mesenchymal-epithelial-transition (MET). While EMT-centric signatures correlate with response to therapy, they are unable to predict metastatic outcome. One reason is due to the wide range of transient phenotypes required for a tumor cell to disseminate and recreate a similar histology at distant sites. Since such dynamic cellular processes are also seen during embryo development (epithelial-like epiblast cells undergo transient EMT to generate the mesoderm, which eventually redifferentiates into epithelial tissues by MET), we sought to utilize this unique and highly conserved property of cellular plasticity to predict metastasis. Here we present the identification of a novel prognostic gene expression signature derived from mouse embryonic day 6.5 that is representative of extensive cellular plasticity, and predicts metastatic competence in human breast tumor cells. This signature may thus complement conventional clinical parameters to offer accurate prediction for outcome among multiple classes of breast cancer patients.
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20
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Zhang M, Cui F, Lu S, Lu H, Xue Y, Wang J, Chen J, Zhao S, Ma S, Zhang Y, Yu Y, Peng Z, Tang H. Developmental pluripotency-associated 4: a novel predictor for prognosis and a potential therapeutic target for colon cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:60. [PMID: 26063247 PMCID: PMC4466839 DOI: 10.1186/s13046-015-0176-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/27/2015] [Indexed: 12/12/2022]
Abstract
Backgrounds Developmental pluripotency-associated 4 (Dppa4) gene plays an important role in self-renewal and pluripotency sustainability in embryonic stem cells. It is re-expressed in several malignant tumors and is identified as a new pluripotency-related oncogene. The present study investigates the expression and clinical significance of Dppa4 in colon cancer. Methods Real-time polymerase chain reaction and Western blotting were used to evaluate Dppa4 mRNA and protein expression in 39 pairs of fresh-frozzen colon cancer samples, which were compared with adjacent normal mucosa. The Dppa4 protein was evaluated by immunohistochemical techniques using colon tissue microarrays (TMA). The sample included 185 cancer specimens and corresponding normal colorectal mucosa. The effect of Dppa4 knockdown on colorectal cancer cell proliferation was investigated using Cell Counting Kit-8 (CCK8) assays and colony-formation assays. Results Both the mRNA and protein level expression of Dppa4 gene was found to be upregulated in colon cancer tissues. Furthermore, the upregulated expression of Dppa4 was significantly correlated with the results of American Joint Committee on Cancer (AJCC) stage (P = 0.01), invasion depth (P = 0.028), nodal involvement (P = 0.012), distant metastasis (P = 0.003), and differentiation (P = 0.002). Dppa4 was also shown to be an independent prognostic indicator of disease-free survival (HR 6.118, 95 % CI 3.004–12.462) and overall survival (HR 6.348, 95 % CI 2.875–14.014) for patients with colon cancer. Knockdown of Dppa4 expression inhibited the proliferation of colorectal cancer cell lines through G1/S transition regulation. Conclusion The results indicate that Dppa4 might play an important role in colon cancer progression and function as a novel prognostic indicator and a potential therapeutic target.
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Affiliation(s)
- Meng Zhang
- Departments of Pathology, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Feifei Cui
- Departments of General Surgery, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Su Lu
- Departments of Pathology, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Huijun Lu
- Departments of Pathology, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Yingming Xue
- Departments of General Surgery, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Jingtao Wang
- Departments of General Surgery, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Jian Chen
- Departments of General Surgery, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Senlin Zhao
- Departments of General Surgery, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Shaofei Ma
- Departments of Pathology, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Yu Zhang
- Departments of Pathology, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Yang Yu
- Departments of General Surgery, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Zhihai Peng
- Departments of General Surgery, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Huamei Tang
- Departments of Pathology, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
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21
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Zhou X, Wang X, Huang Z, Xu L, Zhu W, Liu P. An ER-associated miRNA signature predicts prognosis in ER-positive breast cancer. J Exp Clin Cancer Res 2014; 33:94. [PMID: 25373603 PMCID: PMC4232612 DOI: 10.1186/s13046-014-0094-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 10/27/2014] [Indexed: 11/13/2022] Open
Abstract
Background Breast cancer patients with positive estrogen receptor (ER) have a better prognosis. However, no prognostic miRNA signature was reported in the ER-positive breast cancer. The aim of the study was to identify and assess the prognostic significance of a miRNA signature in ER-positive breast cancer. Methods Two cohorts from The Cancer Genome Atlas (TCGA) dataset were used as training (n =596) and testing set (n =319). Differential expression profiling was identified in the training set. And the prognostic value of the miRNA signature was then assessed in the two cohorts. Results A total of 14 miRNAs were observed to be associated with the status of ER by significance analysis of microarrays (SAM) in the training set. Patients were characterized as high score or low score group according to the calculated risk scores from each miRNA. And patients in high score group had worse overall survival compared with those in low score group both in the training and testing set. Conclusions Our study revealed a miRNA signature including 14 miRNAs associated with ER status which could act as a prognostic marker in ER-positive breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13046-014-0094-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xin Zhou
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Xiaping Wang
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Clinical Diabetes Centre of Jiangsu Province, Nanjing Medical University, Nanjing, 210029, China.
| | - Zebo Huang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Lei Xu
- Department of Thoracic Surgery, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, 210029, China.
| | - Wei Zhu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Ping Liu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China. .,Cancer Center of Nanjing Medical University, Nanjing, 210029, China.
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22
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Meng J, Li P, Zhang Q, Yang Z, Fu S. A four-long non-coding RNA signature in predicting breast cancer survival. J Exp Clin Cancer Res 2014; 33:84. [PMID: 25288503 PMCID: PMC4198622 DOI: 10.1186/s13046-014-0084-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 09/24/2014] [Indexed: 11/12/2022] Open
Abstract
Background Many long non-coding RNAs(lncRNAs) have been found to be a good marker for several tumors. Using lncRNA-mining approach, we aimed to identify lncRNA expression signature that can predict breast cancer patient survival. Methods We performed LncRNA expression profiling in 887 breast cancer patients from Gene Expression Omnibus (GEO) datasets. The association between lncRNA signature and clinical survival was analyzed using the training set(n = 327, from GSE 20685). The validation for the association was performed in another three independent testing sets(252 from GSE21653, 204 from GSE12276, and 104 from GSE42568). Results A set of four lncRNA genes (U79277, AK024118, BC040204, AK000974) have been identified by the random survival forest algorithm. Using a risk score based on the expression signature of these lncRNAs, we separated the patients into low-risk and high-risk groups with significantly different survival times in the training set. This signature was validated in the other three cohorts. Further study revealed that the four-lncRNA expression signature was independent of age and subtype. Gene Set Enrichment Analysis (GSEA) suggested that gene sets were involved in several cancer metastasis related pathways. Conclusions These findings indicate that lncRNAs may be implicated in breast cancer pathogenesis. The four-lncRNA signature may have clinical implications in the selection of high-risk patients for adjuvant therapy. Electronic supplementary material The online version of this article (doi:10.1186/s13046-014-0084-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jin Meng
- Department of Radiation Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yi Shan Rd, Shanghai, 200233, China.
| | - Ping Li
- Department of Radiation Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yi Shan Rd, Shanghai, 200233, China.
| | - Qing Zhang
- Radiation Oncology Center, Fudan University Shanghai Cancer Center (FUSCC), 399 LingLing Rd, Xu Hui District, Shanghai, 200032, China. .,Radiation Oncology Department, Shanghai Proton and Heavy Ion Center (SPHIC), 4365 Kang Xin Rd, Pudong New District, Shanghai, 201321, China.
| | - Zhangru Yang
- Department of Radiation Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yi Shan Rd, Shanghai, 200233, China.
| | - Shen Fu
- Radiation Oncology Center, Fudan University Shanghai Cancer Center (FUSCC), 399 LingLing Rd, Xu Hui District, Shanghai, 200032, China. .,Radiation Oncology Department, Shanghai Proton and Heavy Ion Center (SPHIC), 4365 Kang Xin Rd, Pudong New District, Shanghai, 201321, China.
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