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Yang Z, Jiang Y, Wang L, Yu B, Cai H, Fan J, Zhang M. Prognosis and biological function of SGOL1 in clear cell renal cell carcinoma: a multiomics analysis. BMC Med Genomics 2024; 17:60. [PMID: 38383432 PMCID: PMC10882763 DOI: 10.1186/s12920-024-01825-7] [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: 10/09/2023] [Accepted: 02/06/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Shugoshin-1 (SGOL1) is a mammalian ortholog of Shugoshin in yeast and is essential for precise chromosome segregation during mitosis and meiosis. Aberrant SGOL1 expression was reported to be closely correlated with the malignant progression of various tumors. However, the expression pattern and biological function of SGOL1 in clear cell renal cell carcinoma (ccRCC) are unclear. METHODS The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases provide mRNA expression data and outcome information for ccRCC patients. Immunohistochemistry (IHC) of ccRCC tissue chips verified SGOL1 protein expression in ccRCC patients. Data processing and visualization were performed with the UALCAN, TISIDB, TIMER, GSCA, LinkedOmics, and starBase databases. Gene Ontology (GO) annotation and gene set enrichment analysis (GSEA) were used to identify SGOL1-related biological functions and signaling pathways. Immune infiltration analysis was performed using the TISIDB database, ssGSEA algorithm, and TCGA-KIRC cohort. The biological role of SGOL1 in ccRCC was investigated using a series of in vitro cytological assays, including the MTT assay, EdU staining assay, flow cytometry analysis, Transwell assay, and wound healing assay. RESULTS SGOL1 was highly expressed in ccRCC and linked to adverse clinicopathological parameters and unfavorable prognosis. Multivariate logistic regression and nomogram calibration suggested that SGOL1 might serve as an independent and reliable prognostic predictor of ccRCC. Functional enrichment analysis indicated that SGOL1 may be involved in the cell cycle, the p53 pathway, DNA replication, and T-cell activation. Furthermore, tumor microenvironment (TME) analysis suggested that SGOL1 was positively associated with Treg infiltration and immune checkpoint upregulation. In addition, we identified a potential SNHG17/PVT1/ZMIZ1-AS1-miR-23b-3p-SGOL1 axis correlated with ccRCC carcinogenesis and progression. Finally, we demonstrated that SGOL1 promoted ccRCC cell proliferation, migratory capacity, and invasion in vitro. CONCLUSIONS SGOL1 potentially functions as an oncogene in ccRCC progression and might contribute to the immunosuppressive TME by increasing Treg infiltration and checkpoint expression, suggesting that targeting SGOL1 could be a novel therapeutic strategy for the treatment of ccRCC patients.
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Affiliation(s)
- Zezhong Yang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Address: No.277 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Yunzhong Jiang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Address: No.277 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Lu Wang
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Address: No.277 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Binghe Yu
- Department of Ophthalmology, The First Affiliated Hospital of Xi'an Jiaotong University, Address: No.277 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Hui Cai
- Department of Vascular Surgery, The First Affiliated Hospital of Xi'an Jiaotong University. Address: No, 277 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Jinhai Fan
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Address: No.277 Yanta West Road, Xi'an, Shaanxi, 710061, China.
| | - Mengzhao Zhang
- Department of Vascular Surgery, The First Affiliated Hospital of Xi'an Jiaotong University. Address: No, 277 Yanta West Road, Xi'an, Shaanxi, 710061, China.
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2
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Dai X, Yu L, Chen X, Zhang J. SNRPD1 confers diagnostic and therapeutic values on breast cancers through cell cycle regulation. Cancer Cell Int 2021; 21:229. [PMID: 33879154 PMCID: PMC8059192 DOI: 10.1186/s12935-021-01932-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 04/13/2021] [Indexed: 01/05/2023] Open
Abstract
Background SNRPD1 is a spliceosome-associated protein and has previously been implicated with important roles in cancer development. Methods Through analyzing the differential expression patterns and clinical association of splicing associated genes among tumor and tumor adjacent samples across different tumors and among different breast cancer subtypes, we identify the tumor promotive role of SNRPD1 using multiple publicly available datasets. Through pathway, gene ontology enrichment analysis and network construction, we linked the onco-therapeutic role of SNRPD1 with cell cycle. Via a series of experimental studies including knockdown assay, qPCR, western blotting, cell cycle, drug response assay, we confirmed the higher expression of SNPRD1 at both gene and protein expression levels in triple negative breast cancer cells, as well as its roles in promoting cell cycle and chemotherapy response. Results Our study revealed that SNRPD1 over-expression was significantly associated with genes involved in cell cycle, cell mitosis and chromatin replication, and silencing SNRPD1 in breast cancer cells could lead to halted tumor cell growth and cell cycle arrest at the G0/G1 stage. We also found that triple negative breast cancer cells with reduced SNRPD1 expression lost certain sensitivity to doxorubicin whereas luminal cancer cells did not. Conclusions Our results suggested the prognostic value of SNRPD1 on breast cancer survival, its potential as the therapeutic target halting cell cycle progression for breast cancer control, and warranted special attention on the combined use of doxorubicin and drugs targeting SNRPD1. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-01932-w.
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Affiliation(s)
- Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
| | - Lihui Yu
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiao Chen
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jianying Zhang
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
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3
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Marcel V, Kielbassa J, Marchand V, Natchiar KS, Paraqindes H, Nguyen Van Long F, Ayadi L, Bourguignon-Igel V, Lo Monaco P, Monchiet D, Scott V, Tonon L, Bray SE, Diot A, Jordan LB, Thompson AM, Bourdon JC, Dubois T, André F, Catez F, Puisieux A, Motorin Y, Klaholz BP, Viari A, Diaz JJ. Ribosomal RNA 2'O-methylation as a novel layer of inter-tumour heterogeneity in breast cancer. NAR Cancer 2020; 2:zcaa036. [PMID: 34316693 PMCID: PMC8210124 DOI: 10.1093/narcan/zcaa036] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Recent epitranscriptomics studies unravelled that ribosomal RNA (rRNA) 2′O-methylation is an additional layer of gene expression regulation highlighting the ribosome as a novel actor of translation control. However, this major finding lies on evidences coming mainly, if not exclusively, from cellular models. Using the innovative next-generation RiboMeth-seq technology, we established the first rRNA 2′O-methylation landscape in 195 primary human breast tumours. We uncovered the existence of compulsory/stable sites, which show limited inter-patient variability in their 2′O-methylation level, which map on functionally important sites of the human ribosome structure and which are surrounded by variable sites found from the second nucleotide layers. Our data demonstrate that some positions within the rRNA molecules can tolerate absence of 2′O-methylation in tumoral and healthy tissues. We also reveal that rRNA 2′O-methylation exhibits intra- and inter-patient variability in breast tumours. Its level is indeed differentially associated with breast cancer subtype and tumour grade. Altogether, our rRNA 2′O-methylation profiling of a large-scale human sample collection provides the first compelling evidence that ribosome variability occurs in humans and suggests that rRNA 2′O-methylation might represent a relevant element of tumour biology useful in clinic. This novel variability at molecular level offers an additional layer to capture the cancer heterogeneity and associates with specific features of tumour biology thus offering a novel targetable molecular signature in cancer.
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Affiliation(s)
- Virginie Marcel
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Janice Kielbassa
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, 69008 Lyon, France
| | - Virginie Marchand
- UMS2008 IBSLor CNRS-INSERM-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Kundhavai S Natchiar
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Hermes Paraqindes
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Flora Nguyen Van Long
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Lilia Ayadi
- UMS2008 IBSLor CNRS-INSERM-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Valérie Bourguignon-Igel
- UMS2008 IBSLor CNRS-INSERM-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Piero Lo Monaco
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Déborah Monchiet
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Véronique Scott
- Predictive biomarkers and novel therapeutic strategies Group, Institut Gustave Roussy, University of Paris Sud, INSERM 981, Université Paris Saclay, 114 rue Edouard Vaillant, 94800 Villejuif, France
| | - Laurie Tonon
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, 69008 Lyon, France
| | - Susan E Bray
- Tayside Tissue Bank, Ninewells Hospital and Medical School, NHS Tayside, Dundee DD1 9SY, Scotland, UK
| | - Alexandra Diot
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, Scotland, UK
| | - Lee B Jordan
- Department of Pathology, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - Alastair M Thompson
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, Scotland, UK
| | - Jean-Christophe Bourdon
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, Scotland, UK
| | - Thierry Dubois
- Breast Cancer Biology Group, Translational Research Department, Institut Curie-PSL Research University, 26 rue d'Ulm, 75005 Paris, France
| | - Fabrice André
- Predictive biomarkers and novel therapeutic strategies Group, Institut Gustave Roussy, University of Paris Sud, INSERM 981, Université Paris Saclay, 114 rue Edouard Vaillant, 94800 Villejuif, France
| | - Frédéric Catez
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Alain Puisieux
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Yuri Motorin
- UMS2008 IBSLor CNRS-INSERM-Lorraine University, Biopôle, 9 avenue de la forêt de haye, 54505 Vandoeuvre-les-Nancy, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, CNRS, Inserm, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Alain Viari
- Synergie Lyon Cancer, Gilles Thomas Bioinformatics Platform, Centre Léon Bérard, 69008 Lyon, France
| | - Jean-Jacques Diaz
- Univ Lyon, Université Claude Bernard Lyon 1, Inserm 1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
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4
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Stefanovska B, Vicier CE, Dayris T, Ogryzko V, Scott V, Bouakka I, Delaloge S, Rocca A, Le Saux O, Trédan O, Bachelot T, André F, Fromigué O. Rapalog-Mediated Repression of Tribbles Pseudokinase 3 Regulates Pre-mRNA Splicing. Cancer Res 2020; 80:2190-2203. [PMID: 32245792 DOI: 10.1158/0008-5472.can-19-2366] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/27/2020] [Accepted: 03/24/2020] [Indexed: 11/16/2022]
Abstract
Rapalogs have become standard-of-care in patients with metastatic breast, kidney, and neuroendocrine cancers. Nevertheless, tumor escape occurs after several months in most patients, highlighting the need to understand mechanisms of resistance. Using a panel of cancer cell lines, we show that rapalogs downregulate the putative protein kinase TRIB3 (tribbles pseudokinase 3). Blood samples of a small cohort of patients with cancer treated with rapalogs confirmed downregulation of TRIB3. Downregulation of TRIB3 was mediated by LRRFIP1 independently of mTOR and disrupted its interaction with the spliceosome, where it participated in rapalog-induced deregulation of RNA splicing. Conversely, overexpression of TRIB3 in a panel of cancer cell lines abolished the cytotoxic effects of rapalogs. These findings identify TRIB3 as a key component of the spliceosome, whose repression contributes significantly to the mechanism of resistance to rapalog therapy. SIGNIFICANCE: Independent of mTOR signaling, rapalogs induce cytoxicity by dysregulating spliceosome function via repression of TRIB3, the loss of which may, in the long term, contribute to therapeutic resistance.
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Affiliation(s)
- Bojana Stefanovska
- Inserm, UMR981, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Sud, Orsay, France
| | - Cecile Edith Vicier
- Inserm, UMR981, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Sud, Orsay, France
| | - Thibault Dayris
- Gustave Roussy, Villejuif, France
- Inserm, US23, CNRS, UMS3655, Villejuif, France
| | | | - Veronique Scott
- Inserm, UMR981, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Sud, Orsay, France
| | - Ibrahim Bouakka
- Inserm, UMR981, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Sud, Orsay, France
| | - Suzette Delaloge
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Anna Rocca
- Inserm, UMR981, Villejuif, France
- Gustave Roussy, Villejuif, France
- Université Paris Sud, Orsay, France
| | - Olivia Le Saux
- Department of Medical Oncology, Centre Léon Bérard, Lyon France
| | - Olivier Trédan
- Department of Medical Oncology, Centre Léon Bérard, Lyon France
| | - Thomas Bachelot
- Department of Medical Oncology, Centre Léon Bérard, Lyon France
| | - Fabrice André
- Inserm, UMR981, Villejuif, France
- Gustave Roussy, Villejuif, France
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Olivia Fromigué
- Inserm, UMR981, Villejuif, France.
- Gustave Roussy, Villejuif, France
- Université Paris Sud, Orsay, France
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5
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Nasim N, Ghafouri-Fard S, Soleimani S, Esfandi F, Shirkhoda M, Safaei M, Oskooei VK, Taheri M, Raheb J. Assessment of SGO1 and SGO1-AS1 contribution in breast cancer. Hum Antibodies 2019; 27:279-284. [PMID: 31156154 DOI: 10.3233/hab-190384] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Shugoshin-like protein 1 (SGO1) participated in the proper progression of mitosis. This fundamental role has indicated the importance of this gene in the pathogenesis of cancer as a disorder of mitotic cell division. A previous high throughput study of long non-coding RNAs (lncRNAs) expression in lung cancer has identified aberrant expression of SGO1-antisense 1 (SGO1-AS1) in these specimens. In the current study, we quantified expression of SGO1 and SGO1-AS1 in 39 breast cancer tissues and their paired adjacent non-cancerous tissues (ANCTs). Expression of SGO1-AS1 was considerably decreased in tumoral tissues compared with ANCTs (expression ratio = 0.49, P value = 0.03). However, we could not identify significant difference in expression of SGO1 between these two sets of specimens (expression ratio = 2.9, P value = 0.2). Transcript quantities of SGO1-AS1 were associated with age at disease onset (P= 0.01). Expression of either gene was associated with hormone receptors status or clinical features such as grade and stage. There was an inverse correlation between expressions of genes in both sets of samples. Finally, transcript amounts of SGO1-AS1 could distinguish these two sets of samples with accuracy of 63% (P value = 0.03). Our results imply significance of SGO1-AS1 in breast cancer and necessitate conduction of mechanistic studies to find the molecular pathways in this regard.
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Affiliation(s)
- Negin Nasim
- GenIran Lab, Tashkhis Gene Pajohesh, Tehran, Iran.,GenIran Lab, Tashkhis Gene Pajohesh, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,GenIran Lab, Tashkhis Gene Pajohesh, Tehran, Iran
| | | | | | - Mohammad Shirkhoda
- Department of Oncosurgery, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoomeh Safaei
- Department of Pathology, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Kholghi Oskooei
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamshid Raheb
- National Institute of Genetic Engineering and Biotechnology, Tehran-Karaj Freeway, Tehran, Iran
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6
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Combinatorial expression of microtubule-associated EB1 and ATIP3 biomarkers improves breast cancer prognosis. Breast Cancer Res Treat 2018; 173:573-583. [PMID: 30368744 DOI: 10.1007/s10549-018-5026-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/21/2018] [Indexed: 01/13/2023]
Abstract
PURPOSE The identification of molecular biomarkers for classification of breast cancer is needed to better stratify the patients and guide therapeutic decisions. The aim of this study was to investigate the value of MAPRE1 gene encoding microtubule-end binding proteins EB1 as a biomarker in breast cancer and evaluate whether combinatorial expression of MAPRE1 and MTUS1 gene encoding EB1-negative regulator ATIP3 may improve breast cancer diagnosis and prognosis. METHODS Probeset intensities for MAPRE1 and MTUS1 genes were retrieved from Exonhit splice array analyses of 45 benign and 120 malignant breast tumors for diagnostic purposes. Transcriptomic analyses (U133 Affymetrix array) of one exploratory cohort of 150 invasive breast cancer patients and two independent series of 130 and 155 samples were compared with clinical data of the patients for prognostic studies. A tissue microarray from an independent cohort of 212 invasive breast tumors was immunostained with anti-EB1 and anti-ATIP3 antibodies. RESULTS We show that MAPRE1 gene is a diagnostic and prognostic biomarker in breast cancer. High MAPRE1 levels correlate with tumor malignancy, high histological grade and poor clinical outcome. Combination of high-MAPRE1 and low-MTUS1 levels in tumors is significantly associated with tumor aggressiveness and reduced patient survival. IHC studies of combined EB1/ATIP3 protein expression confirmed these results. CONCLUSIONS These studies emphasize the importance of studying combinatorial expression of EB1 and ATIP3 genes and proteins rather than each biomarker alone. A population of highly aggressive breast tumors expressing high-EB1/low-ATIP3 may be considered for the development of new molecular therapies.
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7
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Franzén B, Kamali-Moghaddam M, Alexeyenko A, Hatschek T, Becker S, Wik L, Kierkegaard J, Eriksson A, Muppani NR, Auer G, Landegren U, Lewensohn R. A fine-needle aspiration-based protein signature discriminates benign from malignant breast lesions. Mol Oncol 2018; 12:1415-1428. [PMID: 30019538 PMCID: PMC6120227 DOI: 10.1002/1878-0261.12350] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 11/05/2022] Open
Abstract
There are increasing demands for informative cancer biomarkers, accessible via minimally invasive procedures, both for initial diagnostics and to follow-up personalized cancer therapy. Fine-needle aspiration (FNA) biopsy provides ready access to relevant tissues; however, the minute sample amounts require sensitive multiplex molecular analysis to achieve clinical utility. We have applied proximity extension assays (PEA) and NanoString (NS) technology for analyses of proteins and of RNA, respectively, in FNA samples. Using samples from patients with breast cancer (BC, n = 25) or benign lesions (n = 33), we demonstrate that these FNA-based molecular analyses (a) can offer high sensitivity and reproducibility, (b) may provide correct diagnosis in shorter time and at a lower cost than current practice, (c) correlate with results from routine analysis (i.e., benchmarking against immunohistochemistry tests for ER, PR, HER2, and Ki67), and (d) may also help identify new markers related to immunotherapy. A specific 11-protein signature, including FGF binding protein 1, decorin, and furin, distinguished all cancer patient samples from all benign lesions in our main cohort and in smaller replication cohort. Due to the minimally traumatic sampling and rich molecular information, this combined proteomics and transcriptomic methodology is promising for diagnostics and evaluation of treatment efficacy in BC.
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Affiliation(s)
- Bo Franzén
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Masood Kamali-Moghaddam
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Andrey Alexeyenko
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.,National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Solna, Sweden
| | - Thomas Hatschek
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Susanne Becker
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.,National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Solna, Sweden
| | - Lotta Wik
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Jonas Kierkegaard
- BröstCentrum City, Stockholm, Sweden.,Capio S:t Görans Sjukhus, Stockholm, Sweden
| | - Annika Eriksson
- KIGene, MMK, Neurogenetics Unit, CMM, Karolinska Institutet, Stockholm, Sweden
| | - Naveen R Muppani
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Gert Auer
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Rolf Lewensohn
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden
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8
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Transcriptional signature of lymphoblastoid cell lines of BRCA1, BRCA2 and non- BRCA1/2 high risk breast cancer families. Oncotarget 2017; 8:78691-78712. [PMID: 29108258 PMCID: PMC5667991 DOI: 10.18632/oncotarget.20219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 07/17/2017] [Indexed: 12/20/2022] Open
Abstract
Approximately 25% of hereditary breast cancer cases are associated with a strong familial history which can be explained by mutations in BRCA1 or BRCA2 and other lower penetrance genes. The remaining high-risk families could be classified as BRCAX (non-BRCA1/2) families. Gene expression involving alternative splicing represents a well-known mechanism regulating the expression of multiple transcripts, which could be involved in cancer development. Thus using RNA-seq methodology, the analysis of transcriptome was undertaken to potentially reveal transcripts implicated in breast cancer susceptibility and development. RNA was extracted from immortalized lymphoblastoid cell lines of 117 women (affected and unaffected) coming from BRCA1, BRCA2 and BRCAX families. Anova analysis revealed a total of 95 transcripts corresponding to 85 different genes differentially expressed (Bonferroni corrected p-value <0.01) between those groups. Hierarchical clustering allowed distinctive subgrouping of BRCA1/2 subgroups from BRCAX individuals. We found 67 transcripts, which could discriminate BRCAX from BRCA1/BRCA2 individuals while 28 transcripts discriminate affected from unaffected BRCAX individuals. To our knowledge, this represents the first study identifying transcripts differentially expressed in lymphoblastoid cell lines from major classes of mutation-related breast cancer subgroups, namely BRCA1, BRCA2 and BRCAX. Moreover, some transcripts could discriminate affected from unaffected BRCAX individuals, which could represent potential therapeutic targets for breast cancer treatment.
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9
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Bjørklund SS, Panda A, Kumar S, Seiler M, Robinson D, Gheeya J, Yao M, Alnæs GIG, Toppmeyer D, Riis M, Naume B, Børresen-Dale AL, Kristensen VN, Ganesan S, Bhanot G. Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma. Sci Rep 2017; 7:5568. [PMID: 28717182 PMCID: PMC5514065 DOI: 10.1038/s41598-017-05537-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 06/05/2017] [Indexed: 12/11/2022] Open
Abstract
Cancer cells can have different patterns of exon usage of individual genes when compared to normal tissue, suggesting that alternative splicing may play a role in shaping the tumor phenotype. The discovery and identification of gene variants has increased dramatically with the introduction of RNA-sequencing technology, which enables whole transcriptome analysis of known, as well as novel isoforms. Here we report alternative splicing and transcriptional events among subtypes of invasive ductal carcinoma in The Cancer Genome Atlas (TCGA) Breast Invasive Carcinoma (BRCA) cohort. Alternative exon usage was widespread, and although common events were shared among three subtypes, ER+ HER2−, ER− HER2−, and HER2+, many events on the exon level were subtype specific. Additional RNA-seq analysis was carried out in an independent cohort of 43 ER+ HER2− and ER− HER2− primary breast tumors, confirming many of the exon events identified in the TCGA cohort. Alternative splicing and transcriptional events detected in five genes, MYO6, EPB41L1, TPD52, IQCG, and ACOX2 were validated by qRT-PCR in a third cohort of 40 ER+ HER2− and ER− HER2− patients, showing that these events were truly subtype specific.
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Affiliation(s)
- Sunniva Stordal Bjørklund
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA.,Department of Cancer Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo, 0310, Norway.,The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, P.O box 1171, Blindern, 0318, Oslo, Norway
| | - Anshuman Panda
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA.,Department of Physics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Surendra Kumar
- Department of Cancer Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo, 0310, Norway.,The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, P.O box 1171, Blindern, 0318, Oslo, Norway.,Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University hospital, Division of Medicine, 1476, Lørenskog, Norway
| | - Michael Seiler
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA.,BioMaPS Institute, Rutgers University, Piscataway, NJ, 08854, USA
| | - Doug Robinson
- BioMaPS Institute, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jinesh Gheeya
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA
| | - Ming Yao
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA
| | - Grethe I Grenaker Alnæs
- Department of Cancer Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo, 0310, Norway
| | - Deborah Toppmeyer
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA
| | - Margit Riis
- Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University hospital, Division of Medicine, 1476, Lørenskog, Norway.,Department of Surgery, Akershus University Hospital, 1478, Lørenskog, Norway.,Department of Breast and Endocrine Surgery, Oslo University Hospital, Ullevål, 0450, Oslo, Norway
| | - Bjørn Naume
- Department of Oncology, Oslo University Hospital, Radiumhospitalet, Oslo, Norway
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo, 0310, Norway.,The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, P.O box 1171, Blindern, 0318, Oslo, Norway
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, OUS Radiumhospitalet, Oslo, 0310, Norway.,The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, P.O box 1171, Blindern, 0318, Oslo, Norway.,Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University hospital, Division of Medicine, 1476, Lørenskog, Norway
| | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA.
| | - Gyan Bhanot
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, 08903, USA. .,Department of Physics, Rutgers University, Piscataway, NJ, 08854, USA. .,Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, NJ, 08854, USA.
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10
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Wu J, Cui Y, Sun X, Cao G, Li B, Ikeda DM, Kurian AW, Li R. Unsupervised Clustering of Quantitative Image Phenotypes Reveals Breast Cancer Subtypes with Distinct Prognoses and Molecular Pathways. Clin Cancer Res 2017; 23:3334-3342. [PMID: 28073839 PMCID: PMC5496801 DOI: 10.1158/1078-0432.ccr-16-2415] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/29/2016] [Accepted: 01/03/2017] [Indexed: 01/28/2023]
Abstract
Purpose: To identify novel breast cancer subtypes by extracting quantitative imaging phenotypes of the tumor and surrounding parenchyma and to elucidate the underlying biologic underpinnings and evaluate the prognostic capacity for predicting recurrence-free survival (RFS).Experimental Design: We retrospectively analyzed dynamic contrast-enhanced MRI data of patients from a single-center discovery cohort (n = 60) and an independent multicenter validation cohort (n = 96). Quantitative image features were extracted to characterize tumor morphology, intratumor heterogeneity of contrast agent wash-in/wash-out patterns, and tumor-surrounding parenchyma enhancement. On the basis of these image features, we used unsupervised consensus clustering to identify robust imaging subtypes and evaluated their clinical and biologic relevance. We built a gene expression-based classifier of imaging subtypes and tested their prognostic significance in five additional cohorts with publically available gene expression data but without imaging data (n = 1,160).Results: Three distinct imaging subtypes, that is, homogeneous intratumoral enhancing, minimal parenchymal enhancing, and prominent parenchymal enhancing, were identified and validated. In the discovery cohort, imaging subtypes stratified patients with significantly different 5-year RFS rates of 79.6%, 65.2%, 52.5% (log-rank P = 0.025) and remained as an independent predictor after adjusting for clinicopathologic factors (HR, 2.79; P = 0.016). The prognostic value of imaging subtypes was further validated in five independent gene expression cohorts, with average 5-year RFS rates of 88.1%, 74.0%, 59.5% (log-rank P from <0.0001 to 0.008). Each imaging subtype was associated with specific dysregulated molecular pathways that can be therapeutically targeted.Conclusions: Imaging subtypes provide complimentary value to established histopathologic or molecular subtypes and may help stratify patients with breast cancer. Clin Cancer Res; 23(13); 3334-42. ©2017 AACR.
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Affiliation(s)
- Jia Wu
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California
| | - Yi Cui
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California
- Global Station for Quantum Medical Science and Engineering, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Proton Beam Therapy Center, Sapporo, Hokkaido, Japan
| | - Xiaoli Sun
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California
- Radiotherapy Department, the First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China
| | - Guohong Cao
- Department of Radiology, International Hospital of Zhejiang University, Hangzhou, Zhejiang, China
| | - Bailiang Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California
| | - Debra M Ikeda
- Department of Radiology, Stanford University School of Medicine, Advanced Medicine Center, Stanford, California
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Allison W Kurian
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
- Department of Medicine, Stanford University School of Medicine, Stanford, California
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California
| | - Ruijiang Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
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11
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Delaloge S, Bonastre J, Borget I, Garbay JR, Fontenay R, Boinon D, Saghatchian M, Mathieu MC, Mazouni C, Rivera S, Uzan C, André F, Dromain C, Boyer B, Pistilli B, Azoulay S, Rimareix F, Bayou EH, Sarfati B, Caron H, Ghouadni A, Leymarie N, Canale S, Mons M, Arfi-Rouche J, Arnedos M, Suciu V, Vielh P, Balleyguier C. The challenge of rapid diagnosis in oncology: Diagnostic accuracy and cost analysis of a large-scale one-stop breast clinic. Eur J Cancer 2016; 66:131-7. [PMID: 27569041 DOI: 10.1016/j.ejca.2016.06.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 05/30/2016] [Accepted: 06/25/2016] [Indexed: 12/16/2022]
Abstract
PURPOSE Rapid diagnosis is a key issue in modern oncology, for which one-stop breast clinics are a model. We aimed to assess the diagnosis accuracy and procedure costs of a large-scale one-stop breast clinic. PATIENTS AND METHODS A total of 10,602 individuals with suspect breast lesions attended the Gustave Roussy's regional one-stop breast clinic between 2004 and 2012. The multidisciplinary clinic uses multimodal imaging together with ultrasonography-guided fine needle aspiration for masses and ultrasonography-guided and stereotactic biopsies as needed. Diagnostic accuracy was assessed by comparing one-stop diagnosis to the consolidated diagnosis obtained after surgery or biopsy or long-term monitoring. The medical cost per patient of the care pathway was assessed from patient-level data collected prospectively. RESULTS Sixty-nine percent of the patients had masses, while 31% had micro-calcifications or other non-mass lesions. In 75% of the cases (87% of masses), an exact diagnosis could be given on the same day. In the base-case analysis (i.e. considering only benign and malignant lesions at one-stop and at consolidated diagnoses), the sensitivity of the one-stop clinic was 98.4%, specificity 99.8%, positive and negative predictive values 99.7% and 99.0%. In the sensitivity analysis (reclassification of suspect, atypical and undetermined lesions), diagnostic sensitivity varied from 90.3% to 98.5% and specificity varied from 94.3% to 99.8%. The mean medical cost per patient of one-stop diagnostic procedure was €420. CONCLUSIONS One-stop breast clinic can provide timely and cost-efficient delivery of highly accurate diagnoses and serve as models of care for multiple settings, including rapid screening-linked diagnosis.
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Affiliation(s)
- Suzette Delaloge
- Gustave Roussy, Université Paris-Saclay, Department of Medical Oncology, Villejuif, F-94805, France.
| | - Julia Bonastre
- Gustave Roussy, Université Paris-Saclay, Department of Biostatistics, Epidemiology and Health Economics, Villejuif, F-94805, France; INSERM U1018, CESP Centre for Research in Epidemiology and Population Health, Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Isabelle Borget
- Gustave Roussy, Université Paris-Saclay, Department of Biostatistics, Epidemiology and Health Economics, Villejuif, F-94805, France; INSERM U1018, CESP Centre for Research in Epidemiology and Population Health, Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Jean-Rémi Garbay
- Gustave Roussy, Université Paris-Saclay, Department of Surgery, Villejuif, F-94805, France
| | - Rachel Fontenay
- Gustave Roussy, Université Paris-Saclay, Department of Biostatistics, Epidemiology and Health Economics, Villejuif, F-94805, France; INSERM U1018, CESP Centre for Research in Epidemiology and Population Health, Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Diane Boinon
- Gustave Roussy, Université Paris-Saclay, Department of Supportive Care, Villejuif, F-94805, France
| | - Mahasti Saghatchian
- Gustave Roussy, Université Paris-Saclay, Department of Medical Oncology, Villejuif, F-94805, France
| | - Marie-Christine Mathieu
- Gustave Roussy, Université Paris-Saclay, Department of Pathology, Villejuif, F-94805, France
| | - Chafika Mazouni
- Gustave Roussy, Université Paris-Saclay, Department of Surgery, Villejuif, F-94805, France
| | - Sofia Rivera
- Gustave Roussy, Université Paris-Saclay, Department of Radiation Therapy, Villejuif, F-94805, France
| | - Catherine Uzan
- Gustave Roussy, Université Paris-Saclay, Department of Surgery, Villejuif, F-94805, France
| | - Fabrice André
- Gustave Roussy, Université Paris-Saclay, Department of Medical Oncology, Villejuif, F-94805, France
| | - Clarisse Dromain
- Gustave Roussy, Université Paris-Saclay, Department of Radiology, Villejuif, F-94805, France
| | - Bruno Boyer
- Gustave Roussy, Université Paris-Saclay, Department of Radiology, Villejuif, F-94805, France
| | - Barbara Pistilli
- Gustave Roussy, Université Paris-Saclay, Department of Medical Oncology, Villejuif, F-94805, France
| | - Sandy Azoulay
- Gustave Roussy, Université Paris-Saclay, Department of Pathology, Villejuif, F-94805, France
| | - Françoise Rimareix
- Gustave Roussy, Université Paris-Saclay, Department of Surgery, Villejuif, F-94805, France
| | - El-Hadi Bayou
- Gustave Roussy, Université Paris-Saclay, Department of Radiology, Villejuif, F-94805, France
| | - Benjamin Sarfati
- Gustave Roussy, Université Paris-Saclay, Department of Surgery, Villejuif, F-94805, France
| | - Hélène Caron
- Gustave Roussy, Université Paris-Saclay, Department of Medical Oncology, Villejuif, F-94805, France
| | - Amal Ghouadni
- Gustave Roussy, Université Paris-Saclay, Department of Medical Oncology, Villejuif, F-94805, France
| | - Nicolas Leymarie
- Gustave Roussy, Université Paris-Saclay, Department of Surgery, Villejuif, F-94805, France
| | - Sandra Canale
- Gustave Roussy, Université Paris-Saclay, Department of Radiology, Villejuif, F-94805, France
| | - Muriel Mons
- Gustave Roussy, Université Paris-Saclay, Department of Medical Information, Villejuif, F-94805, France
| | - Julia Arfi-Rouche
- Gustave Roussy, Université Paris-Saclay, Department of Radiology, Villejuif, F-94805, France
| | - Monica Arnedos
- Gustave Roussy, Université Paris-Saclay, Department of Medical Oncology, Villejuif, F-94805, France
| | - Voichita Suciu
- Gustave Roussy, Université Paris-Saclay, Department of Pathology, Villejuif, F-94805, France
| | - Philippe Vielh
- Gustave Roussy, Université Paris-Saclay, Department of Pathology, Villejuif, F-94805, France
| | - Corinne Balleyguier
- Gustave Roussy, Université Paris-Saclay, Department of Radiology, Villejuif, F-94805, France
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12
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Robinson TJ, Thomas S, Dinan MA, Roman S, Sosa JA, Hyslop T. How Many Lymph Nodes Are Enough? Assessing the Adequacy of Lymph Node Yield for Papillary Thyroid Cancer. J Clin Oncol 2016; 34:3434-9. [PMID: 27528716 DOI: 10.1200/jco.2016.67.6437] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Patients who undergo surgery for papillary thyroid cancer with only a limited lymph node examination are thought to be at risk for potentially harboring occult disease. However, this risk has not been objectively quantified and may have implications for subsequent management and surveillance. METHODS Data from the National Cancer Database (1998 to 2012) were used to characterize the distribution of nodal positivity of adult patients diagnosed with localized ≥ 1-cm papillary thyroid cancer who underwent thyroidectomy with one or more lymph nodes (LNs) examined. A β-binomial distribution was used to estimate the probability of occult nodal disease as a function of total number of LNs examined and pathologic tumor stage. RESULTS A total of 78,724 patients met study criteria; 38,653 patients had node-positive disease. The probability of falsely identifying a patient as node negative was estimated to be 53% for patients with a single node examined and decreased to less than 10% when more than six LNs were examined. To rule out occult nodal disease with 90% confidence, six, nine, and 18 nodes would need to be examined for patients with T1b, T2, and T3 disease, respectively. Sensitivity analyses limited to patients likely undergoing prophylactic central neck dissection resulted in three, four, and eight nodes needed to provide comparable adequacy of LN evaluation. CONCLUSION To our knowledge, our study provides the first empirically based estimates of occult nodal disease risk in patients after surgery for papillary thyroid cancer as a function of primary tumor stage and number of LNs examined. Our estimates provide an objective guideline for evaluating adequacy of LN yield for surgeons and pathologists in the treatment of papillary thyroid cancer, and especially intermediate-risk disease, for which use of adjuvant radioactive iodine and surveillance intensity are not currently standardized.
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13
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Chen HR, Sherr DH, Hu Z, DeLisi C. A network based approach to drug repositioning identifies plausible candidates for breast cancer and prostate cancer. BMC Med Genomics 2016; 9:51. [PMID: 27475327 PMCID: PMC4967295 DOI: 10.1186/s12920-016-0212-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The high cost and the long time required to bring drugs into commerce is driving efforts to repurpose FDA approved drugs-to find new uses for which they weren't intended, and to thereby reduce the overall cost of commercialization, and shorten the lag between drug discovery and availability. We report on the development, testing and application of a promising new approach to repositioning. METHODS Our approach is based on mining a human functional linkage network for inversely correlated modules of drug and disease gene targets. The method takes account of multiple information sources, including gene mutation, gene expression, and functional connectivity and proximity of within module genes. RESULTS The method was used to identify candidates for treating breast and prostate cancer. We found that (i) the recall rate for FDA approved drugs for breast (prostate) cancer is 20/20 (10/11), while the rates for drugs in clinical trials were 131/154 and 82/106; (ii) the ROC/AUC performance substantially exceeds that of comparable methods; (iii) preliminary in vitro studies indicate that 5/5 candidates have therapeutic indices superior to that of Doxorubicin in MCF7 and SUM149 cancer cell lines. We briefly discuss the biological plausibility of the candidates at a molecular level in the context of the biological processes that they mediate. CONCLUSIONS Our method appears to offer promise for the identification of multi-targeted drug candidates that can correct aberrant cellular functions. In particular the computational performance exceeded that of other CMap-based methods, and in vitro experiments indicate that 5/5 candidates have therapeutic indices superior to that of Doxorubicin in MCF7 and SUM149 cancer cell lines. The approach has the potential to provide a more efficient drug discovery pipeline.
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Affiliation(s)
- Hsiao-Rong Chen
- Bioinformatics Program, College of Engineering, Boston University, Boston, MA, USA.,Graduate Program in Translational Molecular Medicine, Boston University School of Medicine, Boston, MA, USA
| | - David H Sherr
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, USA
| | - Zhenjun Hu
- Bioinformatics Program, College of Engineering, Boston University, Boston, MA, USA
| | - Charles DeLisi
- Bioinformatics Program, College of Engineering, Boston University, Boston, MA, USA. .,Department of Biomedical Engineering, Boston University, Boston, MA, USA.
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14
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Bridge JA. Reverse transcription-polymerase chain reaction molecular testing of cytology specimens: Pre-analytic and analytic factors. Cancer Cytopathol 2016; 125:11-19. [DOI: 10.1002/cncy.21762] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Julia A. Bridge
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha Nebraska
- Department of Pediatrics; University of Nebraska Medical Center; Omaha Nebraska
- Department of Orthopedic Surgery; University of Nebraska Medical Center; Omaha Nebraska
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15
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Wang LH, Yen CJ, Li TN, Elowe S, Wang WC, Wang LHC. Sgo1 is a potential therapeutic target for hepatocellular carcinoma. Oncotarget 2015; 6:2023-33. [PMID: 25638162 PMCID: PMC4385833 DOI: 10.18632/oncotarget.2764] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 11/17/2014] [Indexed: 02/07/2023] Open
Abstract
Shugoshin-like protein 1 (Sgo1) is an essential protein in mitosis; it protects sister chromatid cohesion and thereby ensures the fidelity of chromosome separation. We found that the expression of Sgo1 mRNA was relatively low in normal tissues, but was upregulated in 82% of hepatocellular carcinoma (HCC), and correlated with elevated alpha-fetoprotein and early disease onset of HCC. The depletion of Sgo1 reduced cell viability of hepatoma cell lines including HuH7, HepG2, Hep3B, and HepaRG. Using time-lapse microscopy, we showed that hepatoma cells were delayed and ultimately die in mitosis in the absence of Sgo1. In contrast, cell viability and mitotic progression of immortalized cells were not significantly affected. Notably, mitotic cell death induced upon Sgo1 depletion was suppressed upon inhibitions of cyclin-dependent kinase-1 and Aurora kinase-B, or the depletion of mitotic arrest deficient-2. Thus, mitotic cell death induced upon Sgo1 depletion in hepatoma cells is mediated by persistent activation of the spindle assembly checkpoint. Together, these results highlight the essential role of Sgo1 in the maintenance of a proper mitotic progression in hepatoma cells and suggest that Sgo1 is a promising oncotarget for HCC.
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Affiliation(s)
- Lyu-Han Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chia-Jui Yen
- Institute of Clinical Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tian-Neng Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Sabine Elowe
- Université Laval, Faculty of Medicine, Department of Pediatrics, and Reproduction, Perinatal Health, and Infant Health, Québec, Canada
| | - Wen-Ching Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Lily Hui-Ching Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan.,Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan
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16
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Analysis of a FANCE Splice Isoform in Regard to DNA Repair. J Mol Biol 2015; 427:3056-73. [PMID: 26277624 DOI: 10.1016/j.jmb.2015.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 07/15/2015] [Accepted: 08/04/2015] [Indexed: 11/27/2022]
Abstract
The FANC-BRCA DNA repair pathway is activated in response to interstrand crosslinks formed in DNA. A homozygous mutation in 1 of the 17 Fanconi anemia (FA) genes results in malfunctions of this pathway and development of FA syndrome. The integrity of this protein network is essential for good maintenance of DNA repair process and genome stability. Following the identification of an alternatively splice isoform of FANCE (Fanconi anemia complementation group E) significantly expressed in breast cancer individuals from high-risk non-BRCA1/2 families, we studied the impact of this FANCE splice isoform (FANCEΔ4) on DNA repair processes. We have demonstrated that FANCEΔ4 mRNA was efficiently translated into a functional protein and expressed in normal and breast cancer cell lines. Following treatment with the crosslinking agent mitomycin C, EUFA130 (FANCE-deficient) cells infected with FANCEΔ4 were blocked into G2/M phase, while cell survival was significantly reduced compared with FANCE-infected EUFA130 cells. In addition, FANCEΔ4 did not allow FANCD2 and FANCI monoubiquitination, which represents a crucial step of the FANC-BRCA functional pathway. As observed for FANCE wild-type protein, localization of FANCEΔ4 protein was confined to the nucleus following mitomycin C treatment. Although FANCEΔ4 protein showed interaction with FANCE, FANCEΔ4 did not support normal function of FANCE protein in this pathway and could have deleterious effects on FANCE protein activity. We have demonstrated that FANCEΔ4 seems to act as a regulator of FANCD2 protein expression level by promoting its degradation. This study highlights the importance of an efficient regulation of alternative splicing expression of FA genes for proper DNA repair.
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17
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Bjørklund SS, Kristensen VN, Seiler M, Kumar S, Alnæs GIG, Ming Y, Kerrigan J, Naume B, Sachidanandam R, Bhanot G, Børresen-Dale AL, Ganesan S. Expression of an estrogen-regulated variant transcript of the peroxisomal branched chain fatty acid oxidase ACOX2 in breast carcinomas. BMC Cancer 2015; 15:524. [PMID: 26183823 PMCID: PMC4504068 DOI: 10.1186/s12885-015-1510-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/19/2015] [Indexed: 12/05/2022] Open
Abstract
Background Alternate transcripts from a single gene locus greatly enhance the combinatorial flexibility of the human transcriptome. Different patterns of exon usage have been observed when comparing normal tissue to cancers, suggesting that variant transcripts may play a role in the tumor phenotype. Methods Ribonucleic acid-sequencing (RNA-seq) data from breast cancer samples was used to identify an intronic start variant transcript of Acyl-CoA oxidase 2, ACOX2 (ACOX2-i9). Difference in expression between Estrogen Receptor (ER) positive and ER negative patients was assessed by the Wilcoxon rank sum test, and the findings validated in The Cancer Genome Atlas (TCGA) breast cancer dataset (BRCA). ACOX2-i9 expression was also assessed in cell lines using both quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) and Western blot analysis. Knock down by short hairpin RNA (shRNA) and colony formation assays were used to determine whether ACOX2-i9 expression would influence cellular fitness. The effect of ACOX2-i9 expression on patient survival was assessed by the Kaplan-Meier survival function, and association to clinical parameters was analyzed using a Fisher exact test. Results The expression and translation of ACOX2-i9 into a 25 kDa protein was demonstrated in HepG2 cells as well as in several breast cancer cell lines. shRNA knock down of the ACOX2-i9 variant resulted in decreased cell viability of T47D and MDA-MB 436 cells. Moreover, expression of ACOX2-i9 was shown to be estrogen regulated, being induced by propyl pyrazoletriol and inhibited by tamoxifen and fulvestrant in ER+ T47D and Mcf-7 cells, but not in the ER- MDA-MB 436 cell line. This variant transcript showed expression predominantly in ER-positive breast tumors as assessed in our initial set of 53 breast cancers and further validated in 87 tumor/normal pairs from the TCGA breast cancer dataset, and expression was associated with better outcome in ER positive patients. Conclusions ACOX2-i9 is specifically enriched in ER+ breast cancers where expression of the variant is associated with improved outcome. These data identify variant ACOX2 as a potential novel therapeutic biomarker in ER+ breast tumors. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1510-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sunniva Stordal Bjørklund
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumospitalet, Montebello, 0310, Oslo, Norway. .,Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, , 08903, USA. .,The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Vessela N Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumospitalet, Montebello, 0310, Oslo, Norway. .,The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway. .,Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University hospital, Division of Medicine, 1476, Lørenskog, Norway.
| | - Michael Seiler
- Center for Advanced Genomic Technology, Boston University, Boston, MA, 02215, USA.
| | - Surendra Kumar
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumospitalet, Montebello, 0310, Oslo, Norway. .,Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Akershus University hospital, Division of Medicine, 1476, Lørenskog, Norway.
| | - Grethe I Grenaker Alnæs
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumospitalet, Montebello, 0310, Oslo, Norway.
| | - Yao Ming
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, , 08903, USA.
| | - John Kerrigan
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, , 08903, USA.
| | - Bjørn Naume
- The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway. .,Department of Oncology, Oslo University Hospital, Radiumhospitalet, Oslo, Norway.
| | - Ravi Sachidanandam
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, NY, , 10029, USA.
| | - Gyan Bhanot
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, , 08903, USA. .,Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, NJ, , 08854, USA.
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumospitalet, Montebello, 0310, Oslo, Norway. .,The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ, , 08903, USA.
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Peluso AL, Cascone AM, Lucchese L, Cozzolino I, Ieni A, Mignogna C, Pepe S, Zeppa P. Use of FTA cards for the storage of breast carcinoma nucleic acid on fine-needle aspiration samples. Cancer Cytopathol 2015; 123:582-92. [DOI: 10.1002/cncy.21577] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/06/2015] [Accepted: 05/26/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Anna Lucia Peluso
- Department of Medicine and Surgery; University of Salerno; Salerno Italy
| | - Anna Maria Cascone
- Department of Medicine and Surgery; University of Salerno; Salerno Italy
| | - Lucrezia Lucchese
- Department of Medicine and Surgery; University of Salerno; Salerno Italy
| | | | - Antonio Ieni
- Section of Anatomic Pathology, “Gaetano Barresi” Department of Human Pathology; University of Messina; Messina Italy
| | - Chiara Mignogna
- Department of Pathology; Magna Grecia University of Catanzaro; Catanzaro Italy
| | - Stefano Pepe
- Department of Medicine and Surgery; University of Salerno; Salerno Italy
| | - Pio Zeppa
- Department of Medicine and Surgery; University of Salerno; Salerno Italy
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19
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Wen J, Toomer KH, Chen Z, Cai X. Genome-wide analysis of alternative transcripts in human breast cancer. Breast Cancer Res Treat 2015; 151:295-307. [PMID: 25913416 DOI: 10.1007/s10549-015-3395-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 04/16/2015] [Indexed: 12/15/2022]
Abstract
Transcript variants play a critical role in diversifying gene expression. Alternative splicing is a major mechanism for generating transcript variants. A number of genes have been implicated in breast cancer pathogenesis with their aberrant expression of alternative transcripts. In this study, we performed genome-wide analyses of transcript variant expression in breast cancer. With RNA-Seq data from 105 patients, we characterized the transcriptome of breast tumors, by pairwise comparison of gene expression in the breast tumor versus matched healthy tissue from each patient. We identified 2839 genes, ~10 % of protein-coding genes in the human genome, that had differential expression of transcript variants between tumors and healthy tissues. The validity of the computational analysis was confirmed by quantitative RT-PCR assessment of transcript variant expression from four top candidate genes. The alternative transcript profiling led to classification of breast cancer into two subgroups and yielded a novel molecular signature that could be prognostic of patients' tumor burden and survival. We uncovered nine splicing factors (FOX2, MBNL1, QKI, PTBP1, ELAVL1, HNRNPC, KHDRBS1, SFRS2, and TIAR) that were involved in aberrant splicing in breast cancer. Network analyses for the coordinative patterns of transcript variant expression identified twelve "hub" genes that differentiated the cancerous and normal transcriptomes. Dysregulated expression of alternative transcripts may reveal novel biomarkers for tumor development. It may also suggest new therapeutic targets, such as the "hub" genes identified through the network analyses of transcript variant expression, or splicing factors implicated in the formation of the tumor transcriptome.
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Affiliation(s)
- Ji Wen
- Department of Electrical and Computer Engineering, University of Miami, 1251 Memorial Dr, EB406, Coral Gables, FL, 33146, USA
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20
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Martins D, Beca F, Schmitt F. Metastatic breast cancer: mechanisms and opportunities for cytology. Cytopathology 2014; 25:225-30. [PMID: 24889678 DOI: 10.1111/cyt.12158] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2014] [Indexed: 01/15/2023]
Abstract
Despite significant advances in diagnosis, surgical techniques, general patient care, and local and systemic adjuvant therapies, metastatic disease remains the most critical condition limiting the survival of patients with breast cancer. Therefore, the development of effective treatment against late-arising metastasis has become the centre of clinical attention and is one of the current challenges in cancer research. A deeper understanding of the metastatic cascade is fundamental, and the need for repetitive tumour assessments for the evaluation of tumour evolution is a relatively new practice in routine medical care. As such, fine needle aspiration cytology (FNAC) is ideally placed to monitor biological changes in metastasis that may affect treatment and response. As FNAC is a minimally invasive method, it can be performed repeatedly with relatively little trauma, and selective ancillary tests can be applied to FNAC specimens, including for tumour whose primary nature is known. Herein, we review how the linear and parallel models explain metastatic dissemination, thus influencing therapeutic and clinical decisions, and how cytology, together with immunocytochemistry and molecular analysis, can be a tool for routine clinical practice and clinical trials aimed at metastatic disease with a special emphasis on breast cancer.
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Affiliation(s)
- D Martins
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
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21
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Albiges L, Goubar A, Scott V, Vicier C, Lefèbvre C, Alsafadi S, Commo F, Saghatchian M, Lazar V, Dessen P, Delaloge S, André F, Quidville V. Chk1 as a new therapeutic target in triple-negative breast cancer. Breast 2014; 23:250-8. [PMID: 24636978 DOI: 10.1016/j.breast.2014.02.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 01/30/2014] [Accepted: 02/14/2014] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES Bioinformatics analyses of pathways and genes differentially expressed between malignant and benign lesions could allow discovering new therapeutic targets. Here, we identified Checkpoint kinase 1 (Chk1) as a potent therapeutic target in triple-negative breast cancer (TNBC). MATERIALS AND METHODS Differential gene expression between TNBC, other malignant and benign lesions was performed on two breast cancer datasets. Chk1 was targeted using RNA interference or chemical inhibitor in several TNBC cell lines. RESULTS DNA repair pathway was identified as one mostly deregulated pathway in TNBC as compared to benign lesions. Chk1 was identified as candidate target among the 35 genes included in this pathway. Gene expression analysis revealed that Chk1 gene was significantly overexpressed in TNBC as compared to non-TNBC and benign lesions. Depletion of Chk1 protein expression induced a marked reduction of cell viability and led to mitotic catastrophe in TNBC cells. Chemical Chk1 inhibitor decreased survival in TNBC cells, and transcriptome analyze revealed a modulation of gene expression profile in response to Chk1 treatment. CONCLUSION These findings suggest that Chk1 may represent a therapeutic target in TNBC, and provide a rationale to evaluate Chk1 inhibitors in breast cancer patients.
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Affiliation(s)
| | - Aïcha Goubar
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR981, Villejuif F-94800, France
| | - Véronique Scott
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR981, Villejuif F-94800, France
| | - Cécile Vicier
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR981, Villejuif F-94800, France
| | - Céline Lefèbvre
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR981, Villejuif F-94800, France
| | - Samar Alsafadi
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR981, Villejuif F-94800, France
| | - Frédéric Commo
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR981, Villejuif F-94800, France
| | | | - Vladimir Lazar
- Plateforme de Biologie Intégrée, Institut de cancérologie Gustave Roussy, Villejuif F-94800, France
| | - Philippe Dessen
- Plateforme de Biologie Intégrée, Institut de cancérologie Gustave Roussy, Villejuif F-94800, France
| | - Suzette Delaloge
- Department of Medical Oncology, Villejuif F-94800, France; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR981, Villejuif F-94800, France
| | - Fabrice André
- Department of Medical Oncology, Villejuif F-94800, France; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR981, Villejuif F-94800, France.
| | - Virginie Quidville
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR981, Villejuif F-94800, France
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22
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A gene expression and pre-mRNA splicing signature that marks the adenoma-adenocarcinoma progression in colorectal cancer. PLoS One 2014; 9:e87761. [PMID: 24516561 PMCID: PMC3916340 DOI: 10.1371/journal.pone.0087761] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/30/2013] [Indexed: 12/22/2022] Open
Abstract
It is widely accepted that most colorectal cancers (CRCs) arise from colorectal adenomas (CRAs), but transcriptomic data characterizing the progression from colorectal normal mucosa to adenoma, and then to adenocarcinoma are scarce. These transition steps were investigated using microarrays, both at the level of gene expression and alternative pre-mRNA splicing. Many genes and exons were abnormally expressed in CRAs, even more than in CRCs, as compared to normal mucosae. Known biological pathways involved in CRC were altered in CRA, but several new enriched pathways were also recognized, such as the complement and coagulation cascades. We also identified four intersectional transcriptional signatures that could distinguish CRAs from normal mucosae or CRCs, including a signature of 40 genes differentially deregulated in both CRA and CRC samples. A majority of these genes had been described in different cancers, including FBLN1 or INHBA, but only a few in CRC. Several of these changes were also observed at the protein level. In addition, 20% of these genes (i.e. CFH, CRYAB, DPT, FBLN1, ITIH5, NR3C2, SLIT3 and TIMP1) showed altered pre-mRNA splicing in CRAs. As a global variation occurring since the CRA stage, and maintained in CRC, the expression and splicing changes of this 40-gene set may mark the risk of cancer occurrence from analysis of CRA biopsies.
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23
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Adamia S, Haibe-Kains B, Pilarski PM, Bar-Natan M, Pevzner S, Avet-Loiseau H, Lode L, Verselis S, Fox EA, Burke J, Galinsky I, Dagogo-Jack I, Wadleigh M, Steensma DP, Motyckova G, Deangelo DJ, Quackenbush J, Stone R, Griffin JD. A genome-wide aberrant RNA splicing in patients with acute myeloid leukemia identifies novel potential disease markers and therapeutic targets. Clin Cancer Res 2013; 20:1135-45. [PMID: 24284058 DOI: 10.1158/1078-0432.ccr-13-0956] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE Despite new treatments, acute myeloid leukemia (AML) remains an incurable disease. More effective drug design requires an expanded view of the molecular complexity that underlies AML. Alternative splicing of RNA is used by normal cells to generate protein diversity. Growing evidence indicates that aberrant splicing of genes plays a key role in cancer. We investigated genome-wide splicing abnormalities in AML and based on these abnormalities, we aimed to identify novel potential biomarkers and therapeutic targets. EXPERIMENTAL DESIGN We used genome-wide alternative splicing screening to investigate alternative splicing abnormalities in two independent AML patient cohorts [Dana-Farber Cancer Institute (DFCI) (Boston, MA) and University Hospital de Nantes (UHN) (Nantes, France)] and normal donors. Selected splicing events were confirmed through cloning and sequencing analysis, and than validated in 193 patients with AML. RESULTS Our results show that approximately 29% of expressed genes genome-wide were differentially and recurrently spliced in patients with AML compared with normal donors bone marrow CD34(+) cells. Results were reproducible in two independent AML cohorts. In both cohorts, annotation analyses indicated similar proportions of differentially spliced genes encoding several oncogenes, tumor suppressor proteins, splicing factors, and heterogeneous-nuclear-ribonucleoproteins, proteins involved in apoptosis, cell proliferation, and spliceosome assembly. Our findings are consistent with reports for other malignances and indicate that AML-specific aberrations in splicing mechanisms are a hallmark of AML pathogenesis. CONCLUSIONS Overall, our results suggest that aberrant splicing is a common characteristic for AML. Our findings also suggest that splice variant transcripts that are the result of splicing aberrations create novel disease markers and provide potential targets for small molecules or antibody therapeutics for this disease.
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Affiliation(s)
- Sophia Adamia
- Authors' Affiliations: Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada; Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts; Dana-Farber Cancer Institute, Center for Cancer Systems Biology and Department of Genetics, Harvard Medical School, Boston University School of Medicine and Biomedical Engineering Department, Boston University, Boston, Massachusetts; Unité de Génomique du Myélome, Laboratoire UGM, University Hospital, CHU Rangueil, Toulouse, France; Hematology Laboratory, University Hospital; and INSERM U892, Nantes, France; Molecular Diagnostics Laboratory, Dana Farber Cancer Institute, Boston, Massachusetts; Biotique Systems Inc., www.biotiquesystems.com; Adult Leukemia Program, Dana Farber Cancer Institute, Boston, Massachusetts; Brigham and Women's Hospital, Boston, Massachusetts; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
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24
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Pan Y, Luo X, Liu X, Wu LY, Zhang Q, Wang L, Wang W, Zuo L, Wang KS. Genome-wide association studies of maximum number of drinks. J Psychiatr Res 2013; 47:1717-24. [PMID: 23953852 PMCID: PMC4286179 DOI: 10.1016/j.jpsychires.2013.07.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 06/25/2013] [Accepted: 07/18/2013] [Indexed: 12/21/2022]
Abstract
Maximum number of drinks (MaxDrinks) defined as "Maximum number of alcoholic drinks consumed in a 24-h period" is an intermediate phenotype that is closely related to alcohol dependence (AD). Family, twin and adoption studies have shown that the heritability of MaxDrinks is approximately 0.5. We conducted the first genome-wide association (GWA) study and meta-analysis of MaxDrinks as a continuous phenotype. 1059 individuals were from the Collaborative Study on the Genetics of Alcoholism (COGA) sample and 1628 individuals were from the Study of Addiction - Genetics and Environment (SAGE) sample. Family sample with 3137 individuals was from the Australian twin-family study of alcohol use disorder (OZALC). Two population-based Caucasian samples (COGA and SAGE) with 1 million single-nucleotide polymorphisms (SNPs) were used for gene discovery and one family-based Caucasian sample was used for replication. Through meta-analysis we identified 162 SNPs associated with MaxDirnks (p < 10(-4)). The most significant association with MaxDrinks was observed with SNP rs11128951 (p = 4.27 × 10(-8)) near SGOL1 gene at 3p24.3. Furthermore, several SNPs (rs17144687 near DTWD2, rs12108602 near NDST4, and rs2128158 in KCNB2) showed significant associations with MaxDrinks (p < 5 × 10(-7)) in the meta-analysis. Especially, 8 SNPs in DDC gene showed significant associations with MaxDrinks (p < 5 × 10(-7)) in the SAGE sample. Several flanking SNPs in above genes/regions were confirmed in the OZALC family sample. In conclusions, we identified several genes/regions associated with MaxDrinks. These findings can improve the understanding about the pathogenesis of alcohol consumption phenotypes and alcohol-related disorders.
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Affiliation(s)
- Yue Pan
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN, USA
- Department of Epidemiology and Public Health, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Xingguang Luo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Xuefeng Liu
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN, USA
| | - Long-Yang Wu
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 USA
| | - Qunyuan Zhang
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO, USA
| | - Liang Wang
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN, USA
| | - Weize Wang
- Department of Epidemiology and Public Health, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Lingjun Zuo
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Ke-Sheng Wang
- Department of Biostatistics and Epidemiology, College of Public Health, East Tennessee State University, Johnson City, TN, USA
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25
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Eswaran J, Horvath A, Godbole S, Reddy SD, Mudvari P, Ohshiro K, Cyanam D, Nair S, Fuqua SAW, Polyak K, Florea LD, Kumar R. RNA sequencing of cancer reveals novel splicing alterations. Sci Rep 2013; 3:1689. [PMID: 23604310 PMCID: PMC3631769 DOI: 10.1038/srep01689] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 03/01/2013] [Indexed: 12/30/2022] Open
Abstract
Breast cancer transcriptome acquires a myriad of regulation changes, and splicing is critical for the cell to “tailor-make” specific functional transcripts. We systematically revealed splicing signatures of the three most common types of breast tumors using RNA sequencing: TNBC, non-TNBC and HER2-positive breast cancer. We discovered subtype specific differentially spliced genes and splice isoforms not previously recognized in human transcriptome. Further, we showed that exon skip and intron retention are predominant splice events in breast cancer. In addition, we found that differential expression of primary transcripts and promoter switching are significantly deregulated in breast cancer compared to normal breast. We validated the presence of novel hybrid isoforms of critical molecules like CDK4, LARP1, ADD3, and PHLPP2. Our study provides the first comprehensive portrait of transcriptional and splicing signatures specific to breast cancer sub-types, as well as previously unknown transcripts that prompt the need for complete annotation of tissue and disease specific transcriptome.
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Affiliation(s)
- Jeyanthy Eswaran
- McCormick Genomic and Proteomics Center, The George Washington University, Washington, District of Columbia 20037, USA
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26
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Quidville V, Alsafadi S, Goubar A, Commo F, Scott V, Pioche-Durieu C, Girault I, Baconnais S, Le Cam E, Lazar V, Delaloge S, Saghatchian M, Pautier P, Morice P, Dessen P, Vagner S, André F. Targeting the deregulated spliceosome core machinery in cancer cells triggers mTOR blockade and autophagy. Cancer Res 2013; 73:2247-58. [PMID: 23358685 DOI: 10.1158/0008-5472.can-12-2501] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The spliceosome is a large ribonucleoprotein complex that guides pre-mRNA splicing in eukaryotic cells. Here, we determine whether the spliceosome could constitute an attractive therapeutic target in cancer. Analysis of gene expression arrays from lung, breast, and ovarian cancers datasets revealed that several genes encoding components of the core spliceosome composed of a heteroheptameric Sm complex were overexpressed in malignant disease as compared with benign lesions and could also define a subset of highly aggressive breast cancers. siRNA-mediated depletion of SmE (SNRPE) or SmD1 (SNRPD1) led to a marked reduction of cell viability in breast, lung, and melanoma cancer cell lines, whereas it had little effect on the survival of the nonmalignant MCF-10A breast epithelial cells. SNRPE or SNRPD1 depletion did not lead to apoptotic cell death but autophagy, another form of cell death. Indeed, induction of autophagy was revealed by cytoplasmic accumulation of autophagic vacuoles and by an increase in both LC3 (MAP1LC3A) protein conversion and the amount of acidic autophagic vacuoles. Knockdown of SNRPE dramatically decreased mTOR mRNA and protein levels and was accompanied by a deregulation of the mTOR pathway, which, in part, explains the SNRPE-dependent induction of autophagy. These findings provide a rational to develop new therapeutic agents targeting spliceosome core components in oncology.
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Affiliation(s)
- Virginie Quidville
- Institut National de la Santé et de la Recherche Médicale (INSERM) U981, Paris, France
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27
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Ladd JJ, Chao T, Johnson MM, Qiu J, Chin A, Israel R, Pitteri SJ, Mao J, Wu M, Amon LM, McIntosh M, Li C, Prentice R, Disis N, Hanash S. Autoantibody signatures involving glycolysis and splicesome proteins precede a diagnosis of breast cancer among postmenopausal women. Cancer Res 2012; 73:1502-13. [PMID: 23269276 DOI: 10.1158/0008-5472.can-12-2560] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We assessed the autoantibody repertoire of a mouse model engineered to develop breast cancer and the repertoire of autoantibodies in human plasmas collected at a preclinical time point and at the time of clinical diagnosis of breast cancer. In seeking to identify common pathways, networks, and protein families associated with the humoral response, we elucidated the dynamic nature of tumor antigens and autoantibody interactions. Lysate proteins from an immortalized cell line from a MMTV-neu mouse model and from MCF7 human breast cancers were spotted onto nitrocellulose microarrays and hybridized with mouse and human plasma samples, respectively. Immunoglobulin-based plasma immunoreactivity against glycolysis and spliceosome proteins was a predominant feature observed both in tumor-bearing mice and in prediagnostic human samples. Interestingly, autoantibody reactivity was more pronounced further away than closer to diagnosis. We provide evidence for dynamic changes in autoantibody reactivity with tumor development and progression that may depend, in part, on the extent of antigen-antibody interactions.
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Affiliation(s)
- Jon J Ladd
- Fred Hutchinson Cancer Research Center and Tumor Vaccine Group, University of Washington, Seattle, WA 98109, USA
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28
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Graham LD, Pedersen SK, Brown GS, Ho T, Kassir Z, Moynihan AT, Vizgoft EK, Dunne R, Pimlott L, Young GP, Lapointe LC, Molloy PL. Colorectal Neoplasia Differentially Expressed (CRNDE), a Novel Gene with Elevated Expression in Colorectal Adenomas and Adenocarcinomas. Genes Cancer 2012; 2:829-40. [PMID: 22393467 DOI: 10.1177/1947601911431081] [Citation(s) in RCA: 208] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 11/02/2011] [Indexed: 12/13/2022] Open
Abstract
An uncharacterized gene locus (Chr16:hCG_1815491), now named colorectal neoplasia differentially expressed (gene symbol CRNDE), is activated early in colorectal neoplasia. The locus is unrelated to any known protein-coding gene. Microarray analysis of 454 tissue specimens (discovery) and 68 previously untested specimens (validation) showed elevated expression of CRNDE in >90% of colorectal adenomas and adenocarcinomas. These findings were confirmed and extended by exon microarray studies and RT-PCR assays. CRNDE transcription start sites were identified in CaCo2 and HCT116 cells by 5'-RACE. The major transcript isoforms in colorectal cancer (CRC) cell lines and colorectal tissue are CRNDE-a, -b, -d, -e, -f, -h, and -j. Except for CRNDE-d, the known CRNDE splice variants are upregulated in neoplastic colorectal tissue; expression levels for CRNDE-h alone demonstrate a sensitivity of 95% and specificity of 96% for adenoma versus normal tissue. A quantitative RT-PCR assay measuring CRNDE-h RNA levels in plasma was (with a threshold of 2(-ΔCt) = 2.8) positive for 13 of 15 CRC patients (87%) but only 1 of 15 healthy individuals (7%). We conclude that individual CRNDE transcripts show promise as tissue and plasma biomarkers, potentially exhibiting high sensitivity and specificity for colorectal adenomas and cancers.
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Affiliation(s)
- Lloyd D Graham
- CSIRO Food and Nutritional Sciences, Sydney, NSW, Australia
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29
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Diagnostic values of GHSR DNA methylation pattern in breast cancer. Breast Cancer Res Treat 2012; 135:705-13. [DOI: 10.1007/s10549-012-2197-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 08/03/2012] [Indexed: 11/25/2022]
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30
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Annaratone L, Marchiò C, Renzulli T, Castellano I, Cantarella D, Isella C, Macrì L, Mariscotti G, Balmativola D, Cantanna E, Deambrogio C, Pietribiasi F, Arisio R, Schmitt F, Medico E, Sapino A. High-throughput molecular analysis from leftover of fine needle aspiration cytology of mammographically detected breast cancer. Transl Oncol 2012; 5:180-9. [PMID: 22741037 PMCID: PMC3384272 DOI: 10.1593/tlo.11343] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 01/18/2012] [Accepted: 01/19/2012] [Indexed: 01/31/2023] Open
Abstract
We investigated whether residual material from diagnostic smears of fine needle aspirations (FNAs) of mammographically detected breast lesions can be successfully used to extract RNA for reliable gene expression analysis. Twenty-eight patients underwent FNA of breast lesions under ultrasonographic guidance. After smearing slides for cytology, residual cells were rinsed with TRIzol to recover RNA. RNA yield ranged from 0.78 to 88.40 µg per sample. FNA leftovers from 23 nonpalpable breast cancers were selected for gene expression profiling using oligonucleotide microarrays. Clusters generated by global expression profiles partitioned samples in well-distinguished subgroups that overlapped with clusters obtained using "biologic scores" (cytohistologic variables) and differed from clusters based on "technical scores" (RNA/complementary RNA/microarray quality). Microarray profiling used to measure the grade of differentiation and estrogen receptor and ERBB2/HER2 status reflected the results obtained by histology and immunohistochemistry. Given that proliferative status in the FNA material is not always assessable, we designed and performed on FNA leftover a multiprobe genomic signature for proliferation genes that strongly correlated with the Ki67 index examined on histologic material. These findings show that cells residual to cytologic smears of FNA are suitable for obtaining high-quality RNA for high-throughput analysis even when taken from small nonpalpable breast lesions.
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Affiliation(s)
- Laura Annaratone
- Department of Biomedical Sciences and Human Oncology, University of Turin, Turin, Italy
| | - Caterina Marchiò
- Department of Biomedical Sciences and Human Oncology, University of Turin, Turin, Italy
| | - Tommaso Renzulli
- Laboratory of Oncogenomics and Department of Oncological Sciences, Institute for Cancer Research and Treatment, University of Turin, Candiolo, Italy
| | - Isabella Castellano
- Department of Biomedical Sciences and Human Oncology, University of Turin, Turin, Italy
- Breast Unit of the Azienda Ospedaliero-Universitaria San Giovanni Battista di Torino, Turin, Italy
| | - Daniela Cantarella
- Laboratory of Oncogenomics and Department of Oncological Sciences, Institute for Cancer Research and Treatment, University of Turin, Candiolo, Italy
| | - Claudio Isella
- Laboratory of Oncogenomics and Department of Oncological Sciences, Institute for Cancer Research and Treatment, University of Turin, Candiolo, Italy
| | - Luigia Macrì
- Department of Biomedical Sciences and Human Oncology, University of Turin, Turin, Italy
- Breast Unit of the Azienda Ospedaliero-Universitaria San Giovanni Battista di Torino, Turin, Italy
| | - Giovanna Mariscotti
- Breast Unit of the Azienda Ospedaliero-Universitaria San Giovanni Battista di Torino, Turin, Italy
- Institute of Diagnostic and Interventional Radiology, University of Turin, Turin, Italy
| | - Davide Balmativola
- Department of Biomedical Sciences and Human Oncology, University of Turin, Turin, Italy
| | - Elisabetta Cantanna
- Department of Biomedical Sciences and Human Oncology, University of Turin, Turin, Italy
| | - Cristina Deambrogio
- Department of Biomedical Sciences and Human Oncology, University of Turin, Turin, Italy
| | | | - Riccardo Arisio
- Department of Obstetrics and Gynecology, Sant'Anna Hospital, Turin, Italy
| | - Fernando Schmitt
- IPATIMUP: Institute of Molecular Pathology and Immunology of the University of Porto and Medical Faculty of Porto University, Porto, Portugal
| | - Enzo Medico
- Laboratory of Oncogenomics and Department of Oncological Sciences, Institute for Cancer Research and Treatment, University of Turin, Candiolo, Italy
| | - Anna Sapino
- Department of Biomedical Sciences and Human Oncology, University of Turin, Turin, Italy
- Laboratory of Oncogenomics and Department of Oncological Sciences, Institute for Cancer Research and Treatment, University of Turin, Candiolo, Italy
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Allende-Vega N, Dayal S, Agarwala U, Sparks A, Bourdon JC, Saville MK. p53 is activated in response to disruption of the pre-mRNA splicing machinery. Oncogene 2012; 32:1-14. [PMID: 22349816 DOI: 10.1038/onc.2012.38] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this study, we show that interfering with the splicing machinery results in activation of the tumour-suppressor p53. The spliceosome was targeted by small interfering RNA-mediated knockdown of proteins associated with different small nuclear ribonucleoprotein complexes and by using the small-molecule splicing modulator TG003. These interventions cause: the accumulation of p53, an increase in p53 transcriptional activity and can result in p53-dependent G(1) cell cycle arrest. Mdm2 and MdmX are two key repressors of p53. We show that a decrease in MdmX protein level contributes to p53 activation in response to targeting the spliceosome. Interfering with the spliceosome also causes an increase in the rate of degradation of Mdm2. Alterations in splicing are linked with tumour development. There are frequently global changes in splicing in cancer. Our study suggests that p53 activation could participate in protection against potential tumour-promoting defects in the spliceosome. A number of known p53-activating agents affect the splicing machinery and this could contribute to their ability to upregulate p53. Preclinical studies indicate that tumours can be more sensitive than normal cells to small-molecule spliceosome inhibitors. Activation of p53 could influence the selective anti-tumour activity of this therapeutic approach.
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Affiliation(s)
- N Allende-Vega
- Division of Cancer Research, Medical Research Institute, Ninewells Hospital and Medical School, University of Dundee, Angus, UK
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Rizzolo P, Silvestri V, Falchetti M, Ottini L. Inherited and acquired alterations in development of breast cancer. APPLICATION OF CLINICAL GENETICS 2011; 4:145-58. [PMID: 23776375 PMCID: PMC3681186 DOI: 10.2147/tacg.s13226] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Breast cancer is the most common cancer among women, accounting for about 30% of all cancers. In contrast, breast cancer is a rare disease in men, accounting for less than 1% of all cancers. Up to 10% of all breast cancers are hereditary forms, caused by inherited germ-line mutations in "high-penetrance," "moderate-penetrance," and "low-penetrance" breast cancer susceptibility genes. The remaining 90% of breast cancers are due to acquired somatic genetic and epigenetic alterations. A heterogeneous set of somatic alterations, including mutations and gene amplification, are reported to be involved in the etiology of breast cancer. Promoter hypermethylation of genes involved in DNA repair and hormone-mediated cell signaling, as well as altered expression of micro RNAs predicted to regulate key breast cancer genes, play an equally important role as genetic factors in development of breast cancer. Elucidation of the inherited and acquired genetic and epigenetic alterations involved in breast cancer may not only clarify molecular pathways involved in the development and progression of breast cancer itself, but may also have an important clinical and therapeutic impact on improving the management of patients with the disease.
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Affiliation(s)
- Piera Rizzolo
- Department of Molecular Medicine, "La Sapienza" University of Rome, Rome, Italy
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Mehta S, Shelling A, Muthukaruppan A, Lasham A, Blenkiron C, Laking G, Print C. Predictive and prognostic molecular markers for cancer medicine. Ther Adv Med Oncol 2011; 2:125-48. [PMID: 21789130 DOI: 10.1177/1758834009360519] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Over the last 10 years there has been an explosion of information about the molecular biology of cancer. A challenge in oncology is to translate this information into advances in patient care. While there are well-formed routes for translating new molecular information into drug therapy, the routes for translating new information into sensitive and specific diagnostic, prognostic and predictive tests are still being developed. Similarly, the science of using tumor molecular profiles to select clinical trial participants or to optimize therapy for individual patients is still in its infancy. This review will summarize the current technologies for predicting treatment response and prognosis in cancer medicine, and outline what the future may hold. It will also highlight the potential importance of methods that can integrate molecular, histopathological and clinical information into a synergistic understanding of tumor progression. While these possibilities are without doubt exciting, significant challenges remain if we are to implement them with a strong evidence base in a widely available and cost-effective manner.
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Affiliation(s)
- Sunali Mehta
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
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34
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Haakensen VD, Lingjaerde OC, Lüders T, Riis M, Prat A, Troester MA, Holmen MM, Frantzen JO, Romundstad L, Navjord D, Bukholm IK, Johannesen TB, Perou CM, Ursin G, Kristensen VN, Børresen-Dale AL, Helland A. Gene expression profiles of breast biopsies from healthy women identify a group with claudin-low features. BMC Med Genomics 2011; 4:77. [PMID: 22044755 PMCID: PMC3216859 DOI: 10.1186/1755-8794-4-77] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 11/01/2011] [Indexed: 12/02/2022] Open
Abstract
Background Increased understanding of the variability in normal breast biology will enable us to identify mechanisms of breast cancer initiation and the origin of different subtypes, and to better predict breast cancer risk. Methods Gene expression patterns in breast biopsies from 79 healthy women referred to breast diagnostic centers in Norway were explored by unsupervised hierarchical clustering and supervised analyses, such as gene set enrichment analysis and gene ontology analysis and comparison with previously published genelists and independent datasets. Results Unsupervised hierarchical clustering identified two separate clusters of normal breast tissue based on gene-expression profiling, regardless of clustering algorithm and gene filtering used. Comparison of the expression profile of the two clusters with several published gene lists describing breast cells revealed that the samples in cluster 1 share characteristics with stromal cells and stem cells, and to a certain degree with mesenchymal cells and myoepithelial cells. The samples in cluster 1 also share many features with the newly identified claudin-low breast cancer intrinsic subtype, which also shows characteristics of stromal and stem cells. More women belonging to cluster 1 have a family history of breast cancer and there is a slight overrepresentation of nulliparous women in cluster 1. Similar findings were seen in a separate dataset consisting of histologically normal tissue from both breasts harboring breast cancer and from mammoplasty reductions. Conclusion This is the first study to explore the variability of gene expression patterns in whole biopsies from normal breasts and identified distinct subtypes of normal breast tissue. Further studies are needed to determine the specific cell contribution to the variation in the biology of normal breasts, how the clusters identified relate to breast cancer risk and their possible link to the origin of the different molecular subtypes of breast cancer.
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Affiliation(s)
- Vilde D Haakensen
- Dept of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Norway
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Abstract
Numerous studies
report splicing alterations in a multitude of
cancers by using gene-by-gene analysis. However,
understanding of the role of alternative
splicing in cancer is now reaching a new level,
thanks to the use of novel technologies allowing
the analysis of splicing at a large-scale level.
Genome-wide analyses of alternative splicing
indicate that splicing alterations can affect
the products of gene networks involved in key
cellular programs. In addition, many splicing
variants identified as being misregulated in
cancer are expressed in normal tissues. These
observations suggest that splicing programs
contribute to specific cellular programs that
are altered during cancer initiation and
progression. Supporting this model, recent
studies have identified splicing factors
controlling cancer-associated splicing programs.
The characterization of splicing programs and
their regulation by splicing factors will allow
a better understanding of the genetic mechanisms
involved in cancer initiation and progression
and the development of new therapeutic
targets.
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Castaldi PJ, Dahabreh IJ, Ioannidis JPA. An empirical assessment of validation practices for molecular classifiers. Brief Bioinform 2011; 12:189-202. [PMID: 21300697 PMCID: PMC3088312 DOI: 10.1093/bib/bbq073] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 11/02/2010] [Indexed: 12/12/2022] Open
Abstract
Proposed molecular classifiers may be overfit to idiosyncrasies of noisy genomic and proteomic data. Cross-validation methods are often used to obtain estimates of classification accuracy, but both simulations and case studies suggest that, when inappropriate methods are used, bias may ensue. Bias can be bypassed and generalizability can be tested by external (independent) validation. We evaluated 35 studies that have reported on external validation of a molecular classifier. We extracted information on study design and methodological features, and compared the performance of molecular classifiers in internal cross-validation versus external validation for 28 studies where both had been performed. We demonstrate that the majority of studies pursued cross-validation practices that are likely to overestimate classifier performance. Most studies were markedly underpowered to detect a 20% decrease in sensitivity or specificity between internal cross-validation and external validation [median power was 36% (IQR, 21-61%) and 29% (IQR, 15-65%), respectively]. The median reported classification performance for sensitivity and specificity was 94% and 98%, respectively, in cross-validation and 88% and 81% for independent validation. The relative diagnostic odds ratio was 3.26 (95% CI 2.04-5.21) for cross-validation versus independent validation. Finally, we reviewed all studies (n = 758) which cited those in our study sample, and identified only one instance of additional subsequent independent validation of these classifiers. In conclusion, these results document that many cross-validation practices employed in the literature are potentially biased and genuine progress in this field will require adoption of routine external validation of molecular classifiers, preferably in much larger studies than in current practice.
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Affiliation(s)
- Peter J Castaldi
- Institute for Clinical Research and Health Policy Studies at Tufts Medical Center, USA
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Mazouni C, Sneige N, Rouzier R, Balleyguier C, Bevers T, André F, Vielh P, Delaloge S. A nomogram to predict for malignant diagnosis of BI-RADS Category 4 breast lesions. J Surg Oncol 2010; 102:220-4. [PMID: 20740578 DOI: 10.1002/jso.21616] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND AND OBJECTIVE BI-RADS Category classification is the most powerful predictor of breast cancer (BC). However, BI-RADS Category 4 lesions are associated with a highly variable rate of BC. The purpose of this study was to develop and validate a nomogram for the prediction of individual probability of BC in patients with BI-RADS Category 4 lesions. METHODS The study included all patients with BI-RADS Category 4 lesions at screening mammogram, who underwent diagnostic cytology or biopsy and, as needed, surgery or follow-up. Univariate and multivariate logistic regression analyses were used to develop the model and build the nomogram. This nomogram was evaluated on a training set of 170 patients treated at IGR Cancer Center, Paris, France. Nomogram performance was evaluated on an external independent dataset of 188 patients from MDA Cancer Center, Houston, Texas. RESULTS A total of 51 (28.5%) patients in the training set and 73 (42.4%) patients in the validation set were diagnosed with BC. The final, most informative, nomogram included information on patient age (P = 0.04), palpable tumor (P = 0.002), menopausal status (P = 0.32), lesion size (P = 0.81), HRT (P = 0.09), and Gail risk (P = 0.58). The predictive accuracy of the nomogram was 0.716, respectively. The concordance index of the model was 0.66 in the validation set. CONCLUSION The nomogram based on clinical and radiological findings may help inform the patients before surgical explorations, to decrease the number of missed cancer cases but currently cannot replace FNA or biopsy.
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Affiliation(s)
- Chafika Mazouni
- Department of Breast Oncology, Institut Gustave Roussy, Villejuif, France
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38
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Robinson TJ, Dinan MA, Dewhirst M, Garcia-Blanco MA, Pearson JL. SplicerAV: a tool for mining microarray expression data for changes in RNA processing. BMC Bioinformatics 2010; 11:108. [PMID: 20184770 PMCID: PMC2838864 DOI: 10.1186/1471-2105-11-108] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 02/25/2010] [Indexed: 12/22/2022] Open
Abstract
Background Over the past two decades more than fifty thousand unique clinical and biological samples have been assayed using the Affymetrix HG-U133 and HG-U95 GeneChip microarray platforms. This substantial repository has been used extensively to characterize changes in gene expression between biological samples, but has not been previously mined en masse for changes in mRNA processing. We explored the possibility of using HG-U133 microarray data to identify changes in alternative mRNA processing in several available archival datasets. Results Data from these and other gene expression microarrays can now be mined for changes in transcript isoform abundance using a program described here, SplicerAV. Using in vivo and in vitro breast cancer microarray datasets, SplicerAV was able to perform both gene and isoform specific expression profiling within the same microarray dataset. Our reanalysis of Affymetrix U133 plus 2.0 data generated by in vitro over-expression of HRAS, E2F3, beta-catenin (CTNNB1), SRC, and MYC identified several hundred oncogene-induced mRNA isoform changes, one of which recognized a previously unknown mechanism of EGFR family activation. Using clinical data, SplicerAV predicted 241 isoform changes between low and high grade breast tumors; with changes enriched among genes coding for guanyl-nucleotide exchange factors, metalloprotease inhibitors, and mRNA processing factors. Isoform changes in 15 genes were associated with aggressive cancer across the three breast cancer datasets. Conclusions Using SplicerAV, we identified several hundred previously uncharacterized isoform changes induced by in vitro oncogene over-expression and revealed a previously unknown mechanism of EGFR activation in human mammary epithelial cells. We analyzed Affymetrix GeneChip data from over 400 human breast tumors in three independent studies, making this the largest clinical dataset analyzed for en masse changes in alternative mRNA processing. The capacity to detect RNA isoform changes in archival microarray data using SplicerAV allowed us to carry out the first analysis of isoform specific mRNA changes directly associated with cancer survival.
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Affiliation(s)
- Timothy J Robinson
- Molecular Cancer Biology Program, Duke University Medical Center, Durham, USA
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Ruiz-Garcia E, Scott V, Machavoine C, Bidart JM, Lacroix L, Delaloge S, Andre F. Gene expression profiling identifies Fibronectin 1 and CXCL9 as candidate biomarkers for breast cancer screening. Br J Cancer 2010; 102:462-8. [PMID: 20068563 PMCID: PMC2822945 DOI: 10.1038/sj.bjc.6605511] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/21/2009] [Accepted: 11/29/2009] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND There is a need to develop blood-based bioassays for breast cancer (BC) screening. In this study, differential gene expression between BC samples and benign tumours was used to identify candidate biomarkers for blood-based screening. METHODS We identified two proteins (Fibronectin 1 and CXCL9) from a gene expression data set that included 120 BC samples and 45 benign lesions. These proteins fulfil the following criteria: differential gene expression between cancer and benign lesion, protein released in the extracellular medium and stable in the serum, commercially available ELISA kit, ELISA accuracy in a feasibility study. Protein concentrations were determined by ELISA. Blood samples were from normal volunteers (n=119) and early BC patients (n=133). RESULTS Seventy-three per cent of patients had cT1-T2 tumour. Patients had higher CXCL9 and Fibronectin 1 concentrations than volunteers. CXCL9 mean concentration was 851 and 635 pg ml(-1) for patients and volunteers respectively (P=0.013). CXCL9 concentration was significantly higher in patients with estrogen receptor (ER)-negative compared with volunteers (P=0.003), data consistent with gene expression profile. Fibronectin 1 mean concentration was 190 microg ml(-1) for patients and 125 microg ml(-1) for volunteers (P<0.001). Areas under the curve for BC diagnosis were 0.78 and 0.62 for Fibronectin 1 and CXCL9 respectively. A combined score including Fibronectin 1 and CXCL9 dosages presented 53% of sensitivity and 98% of specificity. Similar performances were observed for ER-negative tumours. CONCLUSIONS This study suggests that Fibronectin 1/CXCL9 dosage in serum could screen a significant rate of BC, including ER-negative, and that differential gene expression analysis is a good approach to select candidate biomarkers to set up blood assays cancer screening.
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Affiliation(s)
- E Ruiz-Garcia
- Breast Cancer Translational Research Unit, UPRES EA03535, Université Paris XI, Institut Gustave Roussy, Villejuif, France
| | - V Scott
- Breast Cancer Translational Research Unit, UPRES EA03535, Université Paris XI, Institut Gustave Roussy, Villejuif, France
| | - C Machavoine
- Department of Laboratory Medicine, Institut Gustave Roussy, Villejuif, France
| | - J M Bidart
- Department of Laboratory Medicine, Institut Gustave Roussy, Villejuif, France
| | - L Lacroix
- Department of Laboratory Medicine, Institut Gustave Roussy, Villejuif, France
| | - S Delaloge
- Breast Cancer Translational Research Unit, UPRES EA03535, Université Paris XI, Institut Gustave Roussy, Villejuif, France
- Breast Cancer Unit, Department of Medicine, Institut Gustave Roussy, Villejuif, France
| | - F Andre
- Breast Cancer Translational Research Unit, UPRES EA03535, Université Paris XI, Institut Gustave Roussy, Villejuif, France
- Breast Cancer Unit, Department of Medicine, Institut Gustave Roussy, Villejuif, France
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Mook S, Knauer M, Bueno-de-Mesquita JM, Retel VP, Wesseling J, Linn SC, van’t Veer LJ, Rutgers EJ. Metastatic Potential of T1 Breast Cancer can be Predicted by the 70-gene MammaPrint Signature. Ann Surg Oncol 2010; 17:1406-13. [DOI: 10.1245/s10434-009-0902-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Indexed: 01/21/2023]
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Bourgier C, Ozsahin M, Azria D. Multidisciplinary approach of early breast cancer: the biology applied to radiation oncology. Radiat Oncol 2010; 5:2. [PMID: 20074364 PMCID: PMC2822785 DOI: 10.1186/1748-717x-5-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 01/14/2010] [Indexed: 12/19/2022] Open
Abstract
Early breast cancer treatment is based on a multimodality approach with the application of clinical and histological prognostic factors to determine locoregional and systemic treatments. The entire scientific community is strongly involved in the management of this disease: radiologists for screening and early diagnosis, gynecologists, surgical oncologists and radiation oncologists for locoregional treatment, pathologists and biologists for personalized characterization, genetic counselors for BRCA mutation history and medical oncologists for systemic therapies.Recently, new biological tools have established various prognostic subsets of breast cancer and developed predictive markers for miscellaneous treatments.The aim of this article is to highlight the contribution of biological tools in the locoregional management of early breast cancer.
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Affiliation(s)
- Céline Bourgier
- Département d'Oncologie Radiothérapie, Unité fonctionnelle de Sénologie, Institut Gustave Roussy, Villejuif, France.
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Toward an Alzheimer's disease diagnosis via high‐resolution blood gene expression. Alzheimers Dement 2010; 6:25-38. [DOI: 10.1016/j.jalz.2009.07.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Revised: 07/02/2009] [Accepted: 07/02/2009] [Indexed: 11/21/2022]
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Linn SC, Wesseling J. Molecular tests for breast-cancer diagnosis? Lancet Oncol 2009; 10:314-5. [DOI: 10.1016/s1470-2045(09)70070-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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