1
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Kour A, Sambyal V, Guleria K, Singh NR, Uppal MS, Manjari M, Sudan M. In silico pathway analysis based on chromosomal instability in breast cancer patients. BMC Med Genomics 2020; 13:168. [PMID: 33167967 PMCID: PMC7653868 DOI: 10.1186/s12920-020-00811-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/11/2020] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Complex genomic changes that arise in tumors are a consequence of chromosomal instability. In tumor cells genomic aberrations disrupt core signaling pathways involving various genes, thus delineating of signaling pathways can help understand the pathogenesis of cancer. The bioinformatics tools can further help in identifying networks of interactions between the genes to get a greater biological context of all genes affected by chromosomal instability. METHODS Karyotypic analyses was done in 150 clinically confirmed breast cancer patients and 150 age and gender matched healthy controls after 72 h Peripheral lymphocyte culturing and GTG-banding. Reactome database from Cytoscape software version 3.7.1 was used to perform in-silico analysis (functional interaction and gene enrichment). RESULTS Frequency of chromosomal aberrations (structural and numerical) was found to be significantly higher in patients as compared to controls. The genes harbored by chromosomal regions showing increased aberration frequency in patients were further analyzed in-silico. Pathway analysis on a set of genes that were not linked together revealed that genes HDAC3, NCOA1, NLRC4, COL1A1, RARA, WWTR1, and BRCA1 were enriched in the RNA Polymerase II Transcription pathway which is involved in recruitment, initiation, elongation and dissociation during transcription. CONCLUSION The current study employs the information inferred from chromosomal instability analysis in a non-target tissue for determining the genes and the pathways associated with breast cancer. These results can be further extrapolated by performing either mutation analysis in the genes/pathways deduced or expression analysis which can pinpoint the relevant functional impact of chromosomal instability.
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Affiliation(s)
- Akeen Kour
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Vasudha Sambyal
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India.
| | - Kamlesh Guleria
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Neeti Rajan Singh
- Department of Surgery, Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah, Amritsar, Punjab, India
| | - Manjit Singh Uppal
- Department of Surgery, Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah, Amritsar, Punjab, India
| | - Mridu Manjari
- Department of Pathology, Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah, Amritsar, Punjab, India
| | - Meena Sudan
- Department of Radiotherapy, Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah, Amritsar, Punjab, India
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2
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Kanwar N, Carmine-Simmen K, Nair R, Wang C, Moghadas-Jafari S, Blaser H, Tran-Thanh D, Wang D, Wang P, Wang J, Pasculescu A, Datti A, Mak T, Lewis JD, Done SJ. Amplification of a calcium channel subunit CACNG4 increases breast cancer metastasis. EBioMedicine 2020; 52:102646. [PMID: 32062352 PMCID: PMC7016384 DOI: 10.1016/j.ebiom.2020.102646] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 12/20/2019] [Accepted: 01/15/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Previously, we found that amplification of chromosome 17q24.1-24.2 is associated with lymph node metastasis, tumour size, and lymphovascular invasion in invasive ductal carcinoma. A gene within this amplicon, CACNG4, an L-type voltage-gated calcium channel gamma subunit, is elevated in breast cancers with poor prognosis. Calcium homeostasis is achieved by maintaining low intracellular calcium levels. Altering calcium influx/efflux mechanisms allows tumour cells to maintain homeostasis despite high serum calcium levels often associated with advanced cancer (hypercalcemia) and aberrant calcium signaling. METHODS In vitro 2-D and 3-D assays, and intracellular calcium influx assays were utilized to measure tumourigenic activity in response to altered CANCG4 levels and calcium channel blockers. A chick-CAM model and mouse model for metastasis confirmed these results in vivo. FINDINGS CACNG4 alters cell motility in vitro, induces malignant transformation in 3-dimensional culture, and increases lung-specific metastasis in vivo. CACNG4 functions by closing the channel pore, inhibiting calcium influx, and altering calcium signaling events involving key survival and metastatic pathway genes (AKT2, HDAC3, RASA1 and PKCζ). INTERPRETATION CACNG4 may promote homeostasis, thus increasing the survival and metastatic ability of tumour cells in breast cancer. Our findings suggest an underlying pathway for tumour growth and dissemination regulated by CACNG4 that is significant with respect to developing treatments that target these channels in tumours with aberrant calcium signaling. FUNDING Canadian Breast Cancer Foundation, Ontario; Canadian Institutes of Health Research.
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Affiliation(s)
- Nisha Kanwar
- The Campbell Family for Breast Cancer Research, Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
| | | | - Ranju Nair
- The Campbell Family for Breast Cancer Research, Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Chunjie Wang
- Department of Pathology and Laboratory Medicine, Saskatoon City Hospital, Saskatoon, SK S7K 0M7, Canada
| | - Soode Moghadas-Jafari
- The Campbell Family for Breast Cancer Research, Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Heiko Blaser
- The Campbell Family for Breast Cancer Research, Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Danh Tran-Thanh
- Department of Pathology, Centre Hospitalier de l'Université de Montréal, Montréal, QC H2W 1T8, Canada
| | - Dongyu Wang
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, ON M5S 1A1, Canada
| | - Peiqi Wang
- The Campbell Family for Breast Cancer Research, Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada
| | - Jenny Wang
- Samuel Lunenfeld Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Adrian Pasculescu
- Samuel Lunenfeld Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Alessandro Datti
- Samuel Lunenfeld Research Institute, Mt. Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Agricultural, Food, and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Tak Mak
- The Campbell Family for Breast Cancer Research, Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, ON M5S 1A1, Canada
| | - John D Lewis
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Susan J Done
- The Campbell Family for Breast Cancer Research, Princess Margaret Cancer Centre, Toronto, ON M5G 2M9, Canada; Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada; Department of Medical Biophysics, Faculty of Medicine, University of Toronto, ON M5S 1A1, Canada; Laboratory Medicine Program, Department of Pathology, University Health Network, Toronto General Hospital, 200 Elizabeth Street, 11th floor, Toronto, ON M5G 2C4, Canada.
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3
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Hamdan D, Nguyen TT, Leboeuf C, Meles S, Janin A, Bousquet G. Genomics applied to the treatment of breast cancer. Oncotarget 2019; 10:4786-4801. [PMID: 31413819 PMCID: PMC6677666 DOI: 10.18632/oncotarget.27102] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/05/2019] [Indexed: 12/20/2022] Open
Abstract
Breast cancer remains a major health issue in the world with 1.7 million new cases in 2012 worldwide. It is the second cause of death from cancer in western countries. Genomics have started to modify the treatment of breast cancer, and the developments should become more and more significant, especially in the present era of treatment personalization and with the implementation of new technologies. With molecular signatures, genomics enabled a de-escalation of chemotherapy and personalized treatments of localized forms of estrogen-dependent breast cancers. Genomics can also make a real contribution to constitutional genetics, so as to identify mutations in a panel of candidate genes. In this review, we will discuss the contributions of genomics applied to the treatment of breast cancer, whether already validated contributions or possible future applications linked to research data.
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Affiliation(s)
- Diaddin Hamdan
- Hôpital La Porte Verte, Versailles F-78004, France.,U942, Université Paris-Diderot, INSERM, Paris F-75010, France
| | - Thi Thuy Nguyen
- U942, Université Paris-Diderot, INSERM, Paris F-75010, France.,National Cancer Hospital, Medical Oncology Department 2, Ha Noi 110000, Viet Nam.,Ha Noi Medical University, Oncology Department, Ha Noi 116001, Viet Nam
| | - Christophe Leboeuf
- U942, Université Paris-Diderot, INSERM, Paris F-75010, France.,AP-HP-Hôpital Saint-Louis, Laboratoire de Pathologie, Paris F-75010, France
| | - Solveig Meles
- U942, Université Paris-Diderot, INSERM, Paris F-75010, France
| | - Anne Janin
- U942, Université Paris-Diderot, INSERM, Paris F-75010, France.,AP-HP-Hôpital Saint-Louis, Laboratoire de Pathologie, Paris F-75010, France
| | - Guilhem Bousquet
- U942, Université Paris-Diderot, INSERM, Paris F-75010, France.,AP-HP-Hôpital Avicenne, Service d'Oncologie Médicale, Bobigny F-93000, France.,Université Paris 13, Leonard de Vinci, Villetaneuse F-93430, France
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4
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Behring M, Shrestha S, Manne U, Cui X, Gonzalez-Reymundez A, Grueneberg A, Vazquez AI. Integrated landscape of copy number variation and RNA expression associated with nodal metastasis in invasive ductal breast carcinoma. Oncotarget 2018; 9:36836-36848. [PMID: 30627325 PMCID: PMC6305147 DOI: 10.18632/oncotarget.26386] [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: 02/14/2018] [Accepted: 10/31/2018] [Indexed: 01/01/2023] Open
Abstract
Background Lymph node metastasis (NM) in breast cancer is a clinical predictor of patient outcomes, but how its genetic underpinnings contribute to aggressive phenotypes is unclear. Our objective was to create the first landscape analysis of CNV-associated NM in ductal breast cancer. To assess the role of copy number variations (CNVs) in NM, we compared CNVs and/or associated mRNA expression in primary tumors of patients with NM to those without metastasis. Results We found CNV loss in chromosomes 1, 3, 9, 18, and 19 and gains in chromosomes 5, 8, 12, 14, 16-17, and 20 that were associated with NM and replicated in both databases. In primary tumors, per-gene CNVs associated with NM were ten times more frequent than mRNA expression; however, there were few CNV-driven changes in mRNA expression that differed by nodal status. Overlapping regions of CNV changes and mRNA expression were evident for the CTAGE5 gene. In 8q12, 11q13-14, 20q1, and 17q14-24 regions, there were gene-specific gains in CNV-driven mRNA expression associated with NM. Methods Data on CNV and mRNA expression from the TCGA and the METABRIC consortium of breast ductal carcinoma were utilized to identify CNV-based features associated with NM. Within each dataset, associations were compared across omic platforms to identify CNV-driven variations in gene expression. Only replications across both datasets were considered as determinants of NM. Conclusions Gains in CTAGE5, NDUFC2, EIF4EBP1, and PSCA genes and their expression may aid in early diagnosis of metastatic breast carcinoma and have potential as therapeutic targets.
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Affiliation(s)
- Michael Behring
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Sadeep Shrestha
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Upender Manne
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Department of Pathology and Surgery, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Xiangqin Cui
- Biostatistics Department, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Agustin Gonzalez-Reymundez
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Alexander Grueneberg
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Ana I Vazquez
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA.,Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
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5
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Rausch V, Krieg A, Camps J, Behrens B, Beier M, Wangsa D, Heselmeyer-Haddad K, Baldus SE, Knoefel WT, Ried T, Stoecklein NH. Array comparative genomic hybridization of 18 pancreatic ductal adenocarcinomas and their autologous metastases. BMC Res Notes 2017; 10:560. [PMID: 29110683 PMCID: PMC5674747 DOI: 10.1186/s13104-017-2886-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 10/31/2017] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Mortality rates of pancreatic cancer remain high, which is mainly due to advanced disease and metastasis. We hypothesized that genomic copy number alterations are enriched in metastatic cells compared to autologous primary tumors, which may inform on cancer-related pathways possibly serving as potential targets for specific therapies. We investigated 18 pancreatic ductal adenocarcinomas, including 39 lymph node and 5 distant metastases after surgical resection. Analysis was performed with array-based comparative genomic hybridization (aCGH). RESULTS Metastases acquire a higher frequency of copy number alterations with the highest in distant metastasis (median = 42, lymph node metastases: median = 23, primary tumors: median = 17). In lymph node metastases, gains were prevalent on chromosome bands 8q11.23-q24.3, 12q14.1, 17p12.1, 21q22.12, and losses on 3p21.31, 4p14, 8p23.3-p11.21,17p12-11.2. Genes on amplified regions are involved in cancer-related pathways such as WNT-signaling, also involved in metastasis. CONCLUSIONS Pancreatic cancers show a high degree of intratumor heterogeneity, which could lead to resistance of chemotherapy and worse outcome. ACGH analysis reveals regions preferentially gained or lost in synchronous metastases encoding for genes involved in cancer-related pathways, which could lead to novel therapeutic opportunities.
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Affiliation(s)
- Valentin Rausch
- Department of General, Visceral, and Pediatric Surgery, Heinrich-Heine-University and University Hospital Duesseldorf, Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - Andreas Krieg
- Department of General, Visceral, and Pediatric Surgery, Heinrich-Heine-University and University Hospital Duesseldorf, Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - Jordi Camps
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
- Present Address: Gastrointestinal and Pancreatic Oncology Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Bianca Behrens
- Department of General, Visceral, and Pediatric Surgery, Heinrich-Heine-University and University Hospital Duesseldorf, Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - Manfred Beier
- Institute of Human Genetics and Anthropology, Heinrich-Heine-University and University Hospital, Duesseldorf, Germany
| | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Stephan E. Baldus
- Department of Pathology, Heinrich-Heine-University and University Hospital, Duesseldorf, Germany
| | - Wolfram T. Knoefel
- Department of General, Visceral, and Pediatric Surgery, Heinrich-Heine-University and University Hospital Duesseldorf, Moorenstrasse 5, 40225 Duesseldorf, Germany
| | - Thomas Ried
- Section of Cancer Genomics, Genetics Branch, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Center for Cancer Research, Bethesda, MD USA
| | - Nikolas H. Stoecklein
- Department of General, Visceral, and Pediatric Surgery, Heinrich-Heine-University and University Hospital Duesseldorf, Moorenstrasse 5, 40225 Duesseldorf, Germany
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6
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Molecular Profiling and Significance of Circulating Tumor Cell Based Genetic Signatures. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 994:143-167. [PMID: 28560673 DOI: 10.1007/978-3-319-55947-6_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cancer kills by metastasizing beyond the primary site. Early detection, surgical intervention and other treatments have improved the survival rates of patients with cancer, however, once metastasis occurs, responses to conventional therapies become significantly less effective, and this remains the leading cause of death. Circulating tumor cells (CTCs) are tumor cells that have preferentially disseminated from the primary tumor mass into the hematological system, and are en route to favorable distant sites where if they survive, can develop into metastases. They may be the earliest detectable cells with metastatic ability, and are gaining increasing attention because of their prognostic value in many types of cancers including breast, prostate, colon and lung. Recent technological advances have removed barriers that previously hindered the detection and isolation of these rare cells from blood, and have exponentially improved the genetic resolution at which we can characterize signatures that define CTCs. Some of the most significant observations from such examinations are described here. Firstly, aberrations that were thought to be unique to CTCs are detected at subclonal frequencies within primary tumors with measurable heterogeneity, indicating pre-existing genetic signatures for metastasis. Secondly, these subclonal events are enriched in CTCs and metastases, pointing towards the selection of a more 'fit' component of tumor cells with survival advantages. Lastly, this component of cancer cells may also be the chemoresistant portion that escapes systemic treatment, or acquires resistance during progression of the disease. The future of cancer management may include a standardized method of measuring intratumor heterogeneity of the primary as well as matched CTCs. This will help identify and target rare aberrations within primary tumors that make them more adept to disseminate, and also to monitor the development of treatment resistant subclones as cancer progresses.
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7
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Furet E, Bouchtaoui ME, Feugeas JP, Miquel C, Leboeuf C, Beytout C, Bertheau P, Le Rhun E, Bonneterre J, Janin A, Bousquet G. Increased risk of brain metastases in women with breast cancer and p16 expression in metastatic lymph-nodes. Oncotarget 2017; 8:37332-37341. [PMID: 28445153 PMCID: PMC5514912 DOI: 10.18632/oncotarget.16953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/08/2017] [Indexed: 11/25/2022] Open
Abstract
PURPOSE Metastatic breast cancer is a leading cause of mortality in women, partly on account of brain metastases. However, the mechanisms by which cancer cells cross the blood-brain barrier remain undeciphered. Most molecular studies predicting metastatic risk have been performed on primary breast cancer samples. Here we studied metastatic lymph-nodes from patients with breast cancers to identify markers associated with the occurrence of brain metastases. RESULTS Transcriptomic analyses identified CDKN2A/p16 as a gene potentially associated with brain metastases. MATERIALS AND METHODS Fifty-two patients with HER2-overexpressing or triple-negative breast carcinoma with lymph nodes and distant metastases were included in this study. Transcriptomic analyses were performed on laser-microdissected tumor cells from 28 metastatic lymph-nodes. Supervised analyses compared the transcriptomic profiles of women who developed brain metastases and those who did not. As a validation series, we studied metastatic lymph-nodes from 24 other patients.Immunohistochemistry investigations showed that p16 mean scores were significantly higher in patients with brain metastases than in patients without (7.4 vs. 1.7 respectively, p < 0.01). This result was confirmed on the validation series. Multivariate analyses showed that the p16 score was the only variable positively associated with the risk of brain metastases (p = 0.01).With the same threshold of 5 for p16 scores using a Cox model, overall survival was shorter in women with a p16 score over 5 in both series. CONCLUSIONS The risk of brain metastases in women with HER2-overexpressing or triple-negative breast cancer could be better assessed by studying p16 protein expression on surgically removed axillary lymph-nodes.
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Affiliation(s)
- Elise Furet
- Université Paris Diderot, Inserm, Paris, France
- INSERM, U1165-Paris, France
| | | | - Jean-Paul Feugeas
- INSERM, U1137-Paris, France
- Université de Franche-Comté, Département de Biologie, Besançon, France
| | - Catherine Miquel
- Université Paris Diderot, Inserm, Paris, France
- INSERM, U1165-Paris, France
- Hôpital Saint-Louis, APHP, Service de Pathologie, Paris, France
| | - Christophe Leboeuf
- Université Paris Diderot, Inserm, Paris, France
- INSERM, U1165-Paris, France
| | | | - Philippe Bertheau
- Université Paris Diderot, Inserm, Paris, France
- INSERM, U1165-Paris, France
- Hôpital Saint-Louis, APHP, Service de Pathologie, Paris, France
| | - Emilie Le Rhun
- Centre Oscar Lambret, Département de Sénologie, Lille, France
- CHRU de Lille, Neuro-oncologie, Département de neurochirurgie, Lille, France
- INSERM, Villeneuve d’Ascq, France
| | - Jacques Bonneterre
- Centre Oscar Lambret, Département de Sénologie, Lille, France
- Université Lille 2, Département de Sénologie, Lille, France
| | - Anne Janin
- Université Paris Diderot, Inserm, Paris, France
- INSERM, U1165-Paris, France
- Hôpital Saint-Louis, APHP, Service de Pathologie, Paris, France
| | - Guilhem Bousquet
- Université Paris Diderot, Inserm, Paris, France
- INSERM, U1165-Paris, France
- Université Paris 13, Service d’Oncologie, Villetaneuse, France
- Hôpital Avicenne, APHP, Service d’Oncologie Médicale, Bobigny, France
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8
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Liao M, Li B, Zhang S, Liu Q, Liao W, Xie W, Zhang Y. Relationship between LINC00341 expression and cancer prognosis. Oncotarget 2017; 8:15283-15293. [PMID: 28146429 PMCID: PMC5362486 DOI: 10.18632/oncotarget.14843] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/17/2017] [Indexed: 12/13/2022] Open
Abstract
LINC00341 is a novel long intergenic non-protein coding RNA with unknown functions. In our report, we investigated LINC00341 expression and its prognostic value in cancer patients. DNA over-methylation triggered low expression of LINC00341 and that was associated with poor prognosis in cancers. A meta-analysis further confirmed that high expression of LINC00341 was associated with a better prognosis in cancer patients. Both gene set enrichment analysis and meta-analysis showed that LINC00341 inhibited cancer metastasis. Finally, a large-scale multicentre analysis supported a prognostic value of LINC00341 in cancers.
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Affiliation(s)
- Meijian Liao
- School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China
| | - Bing Li
- School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China
| | - Shikuan Zhang
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China
| | - Qing Liu
- School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China
| | - Weijie Liao
- School of Life Sciences, Tsinghua University, Beijing 100084, P.R. China
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China
| | - Weidong Xie
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China
- Open FIESTA Center, Tsinghua University, Shenzhen 518055, P.R. China
| | - Yaou Zhang
- Key Lab in Healthy Science and Technology, Division of Life Science, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, P.R. China
- Open FIESTA Center, Tsinghua University, Shenzhen 518055, P.R. China
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9
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Cava C, Bertoli G, Castiglioni I. Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential. BMC SYSTEMS BIOLOGY 2015; 9:62. [PMID: 26391647 PMCID: PMC4578257 DOI: 10.1186/s12918-015-0211-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/15/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Development of human cancer can proceed through the accumulation of different genetic changes affecting the structure and function of the genome. Combined analyses of molecular data at multiple levels, such as DNA copy-number alteration, mRNA and miRNA expression, can clarify biological functions and pathways deregulated in cancer. The integrative methods that are used to investigate these data involve different fields, including biology, bioinformatics, and statistics. RESULTS These methodologies are presented in this review, and their implementation in breast cancer is discussed with a focus on integration strategies. We report current applications, recent studies and interesting results leading to the identification of candidate biomarkers for diagnosis, prognosis, and therapy in breast cancer by using both individual and combined analyses. CONCLUSION This review presents a state of art of the role of different technologies in breast cancer based on the integration of genetics and epigenetics, and shares some issues related to the new opportunities and challenges offered by the application of such integrative approaches.
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Affiliation(s)
- Claudia Cava
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
| | - Isabella Castiglioni
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Milan, Italy.
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10
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Kimbung S, Johansson I, Danielsson A, Veerla S, Egyhazi Brage S, Frostvik Stolt M, Skoog L, Carlsson L, Einbeigi Z, Lidbrink E, Linderholm B, Loman N, Malmström PO, Söderberg M, Walz TM, Fernö M, Hatschek T, Hedenfalk I. Transcriptional Profiling of Breast Cancer Metastases Identifies Liver Metastasis-Selective Genes Associated with Adverse Outcome in Luminal A Primary Breast Cancer. Clin Cancer Res 2015; 22:146-57. [PMID: 26276891 DOI: 10.1158/1078-0432.ccr-15-0487] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 07/26/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE The complete molecular basis of the organ-specificity of metastasis is elusive. This study aimed to provide an independent characterization of the transcriptional landscape of breast cancer metastases with the specific objective to identify liver metastasis-selective genes of prognostic importance following primary tumor diagnosis. EXPERIMENTAL DESIGN A cohort of 304 women with advanced breast cancer was studied. Associations between the site of recurrence and clinicopathologic features were investigated. Fine-needle aspirates of metastases (n = 91) were subjected to whole-genome transcriptional profiling. Liver metastasis-selective genes were identified by significance analysis of microarray (SAM) analyses and independently validated in external datasets. Finally, the prognostic relevance of the liver metastasis-selective genes in primary breast cancer was tested. RESULTS Liver relapse was associated with estrogen receptor (ER) expression (P = 0.002), luminal B subtype (P = 0.01), and was prognostic for an inferior postrelapse survival (P = 0.01). The major variation in the transcriptional landscape of metastases was also associated with ER expression and molecular subtype. However, liver metastases displayed unique transcriptional fingerprints, characterized by downregulation of extracellular matrix (i.e., stromal) genes. Importantly, we identified a 17-gene liver metastasis-selective signature, which was significantly and independently prognostic for shorter relapse-free (P < 0.001) and overall (P = 0.001) survival in ER-positive tumors. Remarkably, this signature remained independently prognostic for shorter relapse-free survival (P = 0.001) among luminal A tumors. CONCLUSIONS Extracellular matrix (stromal) genes can be used to partition breast cancer by site of relapse and may be used to further refine prognostication in ER positive primary breast cancer.
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Affiliation(s)
- Siker Kimbung
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund, Lund University, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Ida Johansson
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund, Lund University, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Anna Danielsson
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Srinivas Veerla
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund, Lund University, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Suzanne Egyhazi Brage
- Department of Oncology and Pathology, Karolinska Institutet and Karolinska University Hospital, Sweden
| | - Marianne Frostvik Stolt
- Department of Oncology and Pathology, Karolinska Institutet and Karolinska University Hospital, Sweden
| | - Lambert Skoog
- Department of Oncology and Pathology, Karolinska Institutet and Karolinska University Hospital, Sweden
| | - Lena Carlsson
- Department of Oncology, Sundsvall Hospital, Sundsvall, Sweden
| | - Zakaria Einbeigi
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Elisabet Lidbrink
- Department of Oncology and Pathology, Karolinska Institutet and Karolinska University Hospital, Sweden
| | - Barbro Linderholm
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Niklas Loman
- Department of Oncology, Skåne University Hospital, Lund/Malmö, Sweden
| | | | - Martin Söderberg
- Department of Oncology, Skåne University Hospital, Lund/Malmö, Sweden
| | - Thomas M Walz
- Division of Oncology, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden
| | - Mårten Fernö
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund, Lund University, Sweden
| | - Thomas Hatschek
- Department of Oncology and Pathology, Karolinska Institutet and Karolinska University Hospital, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund, Lund University, Sweden. CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden.
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11
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Kanwar N, Hu P, Bedard P, Clemons M, McCready D, Done SJ. Identification of genomic signatures in circulating tumor cells from breast cancer. Int J Cancer 2015; 137:332-44. [PMID: 25529931 DOI: 10.1002/ijc.29399] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 12/04/2014] [Indexed: 12/13/2022]
Abstract
Levels of circulating tumor cells (CTCs) in blood have prognostic value in early and metastatic breast cancer. CTCs also show varying degrees of concordance with molecular markers of primary tumors they originate from. It is expected that individual cells reflect the heterogeneity and evolution of tumor cells as they acquire new functions and differential responses to chemotherapy. However, a degree of commonality is also plausible, highlighting alterations that allow tumor cells to perform CTC-defining activities such as invasion and intravasation. Using a matched tumor-normal approach, we performed high-resolution copy number profiling of CTCs from breast cancer to identify occult changes occurring during progression to metastasis. We identified a signature of recurrent gain in CTCs, consisting of 90 minimal common regions (MCRs) of copy number gain. These were predominantly found across chromosome 19 and were identified at low frequencies (3-4%) in 787 primary breast carcinomas examined. CTC genomic signatures clustered into two groups independent of subtype: a dormancy-related signature with 16 MCRs (AKT2, PTEN, CADM2); and a tumor-aggressiveness related signature with 358 MCRs (ANGPTL4, BSG, MIR-373). There were two MCRs in common between the groups on 19q13 and 21q21, containing genes involved in resistance to anoikis, TGFβ-signaling and metastasis (TFF3, LTBP4, NUMBL). Furthermore, a region harboring the ERBB2 gene was gained in a majority of patients. Regions 20q13 and 15q24 were associated with distant metastasis. The distinctiveness of CTC signatures highlights cell populations with different functional or metastatic potential. Such novel targets could help to specifically identify and block dissemination.
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Affiliation(s)
- Nisha Kanwar
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,The Campbell Family Institute for Breast Cancer Research at the Princess Margaret Cancer Centre, Toronto, Canada
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics, George and Fay Yee Centre for Healthcare Innovation, University of Manitoba, Winnipeg, Canada
| | - Philippe Bedard
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada
| | - Mark Clemons
- Division of Medical Oncology, The Ottawa Hospital Cancer Center, Ottawa, Canada
| | - David McCready
- Division of General Surgery and Surgical Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, Canada
| | - Susan J Done
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,The Campbell Family Institute for Breast Cancer Research at the Princess Margaret Cancer Centre, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Laboratory Medicine Program, University Health Network, Toronto, Canada
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12
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Vollebergh MA, Klijn C, Schouten PC, Wesseling J, Israeli D, Ylstra B, Wessels LF, Jonkers J, Linn SC. Lack of genomic heterogeneity at high-resolution aCGH between primary breast cancers and their paired lymph node metastases. PLoS One 2014; 9:e103177. [PMID: 25083859 PMCID: PMC4118860 DOI: 10.1371/journal.pone.0103177] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 06/29/2014] [Indexed: 11/18/2022] Open
Abstract
Lymph-node metastasis (LNM) predict high recurrence rates in breast cancer patients. Systemic treatment aims to eliminate (micro)metastatic cells. However decisions regarding systemic treatment depend largely on clinical and molecular characteristics of primary tumours. It remains, however, unclear to what extent metastases resemble the cognate primary breast tumours, especially on a genomic level, and as such will be eradicated by the systemic therapy chosen. In this study we used high-resolution aCGH to investigate DNA copy number differences between primary breast cancers and their paired LNMs. To date, no recurrent LNM-specific genomic aberrations have been identified using array comparative genomic hybridization (aCGH) analysis. In our study we employ a high-resolution platform and we stratify on different breast cancer subtypes, both aspects that might have underpowered previously performed studies.To test the possibility that genomic instability in triple-negative breast cancers (TNBCs) might cause increased random and potentially also recurrent copy number aberrations (CNAs) in their LNMs, we studied 10 primary TNBC–LNM pairs and 10 ER-positive (ER+) pairs and verified our findings adding additionally 5 TNBC-LNM and 22 ER+-LNM pairs. We found that all LNMs clustered nearest to their matched tumour except for two cases, of which one was due to the presence of two distinct histological components in one tumour. We found no significantly altered CNAs between tumour and their LNMs in the entire group or in the subgroups. Within the TNBC subgroup, no absolute increase in CNAs was found in the LNMs compared to their primary tumours, suggesting that increased genomic instability does not lead to more CNAs in LNMs. Our findings suggest a high clonal relationship between primary breast tumours and its LNMs, at least prior to treatment, and support the use of primary tumour characteristics to guide adjuvant systemic chemotherapy in breast cancer patients.
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Affiliation(s)
- Marieke A. Vollebergh
- Division of Molecular Pathology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Division of Medical Oncology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Christiaan Klijn
- Division of Molecular Pathology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Philip C. Schouten
- Division of Molecular Pathology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Jelle Wesseling
- Department of Pathology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Danielle Israeli
- Department of Pathology, Vrije Universiteit University Medical Center, Amsterdam, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Vrije Universiteit University Medical Center, Amsterdam, the Netherlands
| | - Lodewyk F.A. Wessels
- Department of Bioinformatics and Statistics, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands
| | - Jos Jonkers
- Division of Molecular Pathology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Sabine C. Linn
- Division of Molecular Pathology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Division of Medical Oncology, Netherlands Cancer Institute–Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- * E-mail:
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13
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Salhia B, Kiefer J, Ross JTD, Metapally R, Martinez RA, Johnson KN, DiPerna DM, Paquette KM, Jung S, Nasser S, Wallstrom G, Tembe W, Baker A, Carpten J, Resau J, Ryken T, Sibenaller Z, Petricoin EF, Liotta LA, Ramanathan RK, Berens ME, Tran NL. Integrated genomic and epigenomic analysis of breast cancer brain metastasis. PLoS One 2014; 9:e85448. [PMID: 24489661 PMCID: PMC3906004 DOI: 10.1371/journal.pone.0085448] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 11/26/2013] [Indexed: 11/19/2022] Open
Abstract
The brain is a common site of metastatic disease in patients with breast cancer, which has few therapeutic options and dismal outcomes. The purpose of our study was to identify common and rare events that underlie breast cancer brain metastasis. We performed deep genomic profiling, which integrated gene copy number, gene expression and DNA methylation datasets on a collection of breast brain metastases. We identified frequent large chromosomal gains in 1q, 5p, 8q, 11q, and 20q and frequent broad-level deletions involving 8p, 17p, 21p and Xq. Frequently amplified and overexpressed genes included ATAD2, BRAF, DERL1, DNMTRB and NEK2A. The ATM, CRYAB and HSPB2 genes were commonly deleted and underexpressed. Knowledge mining revealed enrichment in cell cycle and G2/M transition pathways, which contained AURKA, AURKB and FOXM1. Using the PAM50 breast cancer intrinsic classifier, Luminal B, Her2+/ER negative, and basal-like tumors were identified as the most commonly represented breast cancer subtypes in our brain metastasis cohort. While overall methylation levels were increased in breast cancer brain metastasis, basal-like brain metastases were associated with significantly lower levels of methylation. Integrating DNA methylation data with gene expression revealed defects in cell migration and adhesion due to hypermethylation and downregulation of PENK, EDN3, and ITGAM. Hypomethylation and upregulation of KRT8 likely affects adhesion and permeability. Genomic and epigenomic profiling of breast brain metastasis has provided insight into the somatic events underlying this disease, which have potential in forming the basis of future therapeutic strategies.
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Affiliation(s)
- Bodour Salhia
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- * E-mail: (BS); (NLT)
| | - Jeff Kiefer
- Collaborative Center for Bioinformatics, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Julianna T. D. Ross
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Raghu Metapally
- Collaborative Center for Bioinformatics, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Rae Anne Martinez
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Kyle N. Johnson
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Danielle M. DiPerna
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Kimberly M. Paquette
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Sungwon Jung
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Sara Nasser
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Garrick Wallstrom
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, United States of America
| | - Waibhav Tembe
- Collaborative Center for Bioinformatics, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Angela Baker
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - John Carpten
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Jim Resau
- The Van Andel Research Institute, Grand Rapids, Michigan, United States of America
| | - Timothy Ryken
- Iowa Spine and Brain Institute, Iowa City, Iowa, United States of America
| | - Zita Sibenaller
- Department of Radiation Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, United States of America
| | - Lance A. Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, United States of America
| | - Ramesh K. Ramanathan
- Virginia G. Piper Cancer Center, Scottsdale Healthcare, Scottsdale, Arizona, United States of America
| | - Michael E. Berens
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Nhan L. Tran
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
- * E-mail: (BS); (NLT)
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14
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Wikman H, Sielaff-Frimpong B, Kropidlowski J, Witzel I, Milde-Langosch K, Sauter G, Westphal M, Lamszus K, Pantel K. Clinical relevance of loss of 11p15 in primary and metastatic breast cancer: association with loss of PRKCDBP expression in brain metastases. PLoS One 2012; 7:e47537. [PMID: 23118876 PMCID: PMC3485301 DOI: 10.1371/journal.pone.0047537] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 09/12/2012] [Indexed: 11/18/2022] Open
Abstract
The occurrence of brain metastases among breast cancer patients is currently rising with approximately 20-25% incidence rates, underlining the importance of the identification of new therapeutic and prognostic markers. We have previously screened for new markers for brain metastasis by array CGH. We found that loss of 11p15 is common among these patients. In this study, we investigated the clinical significance of loss of 11p15 in primary breast cancer (BC) and breast cancer brain metastases (BCBM). 11p15 aberration patterns were assessed by allelic imbalance (AI) analysis in primary BC (n = 78), BCBM (n = 21) and metastases from other distant sites (n = 6) using six different markers. AI at 11p15 was significantly associated with BCBM (p = 0.002). Interestingly, a subgroup of primary BC with a later relapse to the brain had almost equally high AI rates as the BCBM cases. In primary BC, AI was statistically significantly associated with high grade, negative hormone receptor status, and triple-negative (TNBC) tumors. Gene expression profiling identified PRKCDBP in the 11p15 region to be significantly downregulated in both BCBM and primary BC with brain relapse compared to primary tumors without relapse or bone metastasis (fdr<0.05). qRT-PCR confirmed these results and methylation was shown to be a common way to silence this gene. In conclusion, we found loss at 11p15 to be a marker for TNBC primary tumors and BCBM and PRKCDBP to be a potential target gene in this locus.
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Affiliation(s)
- Harriet Wikman
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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15
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Liao S, Desouki MM, Gaile DP, Shepherd L, Nowak NJ, Conroy J, Barry WT, Geradts J. Differential copy number aberrations in novel candidate genes associated with progression from in situ to invasive ductal carcinoma of the breast. Genes Chromosomes Cancer 2012; 51:1067-78. [PMID: 22887771 DOI: 10.1002/gcc.21991] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 07/06/2012] [Indexed: 12/21/2022] Open
Abstract
Only a minority of intraductal carcinomas of the breast give rise to stromally invasive disease. We microdissected 206 paraffin blocks representing 116 different cases of low-grade ductal carcinoma in situ (DCIS). Fifty-five were pure DCIS (PD) cases without progression to invasive carcinoma. Sixty-one cases had a small invasive component. DNA was extracted from microdissected sections and hybridized to high-density bacterial artificial chromosome arrays. Array comparative genomic hybridization analysis of 118 hybridized DNA samples yielded data on 69 samples that were suitable for further statistical analysis. This cohort included 20 pure DCIS cases, 25 mixed DCIS (MD), and 24 mixed invasive carcinoma samples. PD cases had a higher frequency of DNA copy number changes than MD cases, and the latter had similar DNA profiles compared to paired invasive carcinomas. Copy number changes on 13 chromosomal arms occurred at different rates in PD versus MD lesions. Eight of 19 candidate genes residing at those loci were confirmed to have differential copy number changes by quantitative PCR. NCOR2/SMRT and NR4A1 (both on 12q), DYNLRB2 (16q), CELSR1, UPK3A, and ST13 (all on 22q) were more frequently amplified in PD. Moreover, NCOR2, NR4A1, and DYNLRB2 showed more frequent copy number losses in MD. GRAP2 (22q) was more often amplified in MD, whereas TAF1C (16q) was more commonly deleted in PD. A multigene model comprising these candidate genes discriminated between PD and MD lesions with high accuracy. These findings suggest that the propensity to invade the stroma may be encoded in the genome of intraductal carcinomas.
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Affiliation(s)
- Shaoxi Liao
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
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16
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Wikman H, Lamszus K, Detels N, Uslar L, Wrage M, Benner C, Hohensee I, Ylstra B, Eylmann K, Zapatka M, Sauter G, Kemming D, Glatzel M, Müller V, Westphal M, Pantel K. Relevance of PTEN loss in brain metastasis formation in breast cancer patients. Breast Cancer Res 2012; 14:R49. [PMID: 22429330 PMCID: PMC3446383 DOI: 10.1186/bcr3150] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 02/16/2012] [Accepted: 03/19/2012] [Indexed: 01/03/2023] Open
Abstract
INTRODUCTION With the improvement of therapeutic options for the treatment of breast cancer, the development of brain metastases has become a major limitation to life expectancy in many patients. Therefore, our aim was to identify molecular markers associated with the development of brain metastases in breast cancer. METHODS Patterns of chromosomal aberrations in primary breast tumors and brain metastases were compared with array-comparative genetic hybridization (CGH). The most significant region was further characterized in more detail by microsatellite and gene-expression analysis, and finally, the possible target gene was screened for mutations. RESULTS The array CGH results showed that brain metastases, in general, display similar chromosomal aberrations as do primary tumors, but with a notably higher frequency. Statistically significant differences were found at nine different chromosomal loci, with a gain and amplification of EGFR (7p11.2) and a loss of 10q22.3-qter being among the most significant aberrations in brain metastases (P < 0.01; false discovery rate (fdr) < 0.04). Allelic imbalance (AI) patterns at 10q were further verified in 77 unmatched primary tumors and 21 brain metastases. AI at PTEN loci was found significantly more often in brain metastases (52%) and primary tumors with a brain relapse (59%) compared with primary tumors from patients without relapse (18%; P = 0.003) or relapse other than brain tumors (12%; P = 0.006). Loss of PTEN was especially frequent in HER2-negative brain metastases (64%). Furthermore, PTEN mRNA expression was significantly downregulated in brain metastases compared with primary tumors, and PTEN mutations were frequently found in brain metastases. CONCLUSIONS These results demonstrate that brain metastases often show very complex genomic-aberration patterns, suggesting a potential role of PTEN and EGFR in brain metastasis formation.
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Affiliation(s)
- Harriet Wikman
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistreet 52, 20246 Hamburg, Germany.
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17
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Desouki MM, Liao S, Conroy J, Nowak NJ, Shepherd L, Gaile DP, Geradts J. The genomic relationship between primary breast carcinomas and their nodal metastases. Cancer Invest 2011; 29:300-7. [PMID: 21469979 DOI: 10.3109/07357907.2011.568564] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We screened the whole tumor genome to identify DNA copy number gains and losses that discriminate between primary breast carcinomas (MP) and their nodal metastases (ML). Six candidate genes were confirmed by quantitative PCR to have differentially distributed copy number changes. Three of the genes (ERRγ, DDX6, and TIAM1) were more commonly amplified in nodal metastases. Principal component analysis revealed that MP-ML pairs varied markedly in their genomic divergence. The latter was larger in PR-negative tumors. Nodal metastases may form early or late in the development of breast carcinomas and PR-negative tumors may metastasize earlier or are genomically less stable.
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Affiliation(s)
- Mohamed M Desouki
- Department of Pathology, Medical University of South Carolina, Charleston, South Carolina, USA
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18
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Desouki MM, Liao S, Huang H, Conroy J, Nowak NJ, Shepherd L, Gaile DP, Geradts J. Identification of metastasis-associated breast cancer genes using a high-resolution whole genome profiling approach. J Cancer Res Clin Oncol 2010; 137:795-809. [PMID: 20680643 DOI: 10.1007/s00432-010-0937-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Accepted: 07/05/2010] [Indexed: 01/23/2023]
Abstract
PURPOSE We employed a whole genome tumor profiling approach in an attempt to identify DNA copy number alterations (CNAs) and new candidate genes that are correlated with the metastatic potential of a primary breast carcinoma and with progression at the metastatic site. METHODS Fifty-four small (≤ 2 cm), high grade, ER-positive, formalin-fixed invasive ductal carcinomas were suitable for whole genome profiling analysis. Twenty-four of them did not form metastases within 5-10 years (unmatched primaries, UP). Thirty tumors had at least one synchronous axillary lymph node metastasis (matched primaries, MP; matched lymph node metastases, ML). Genomic DNA was hybridized to high density (19k) BAC arrays. Statistical analysis revealed differential distributions of CNAs between UP and MP and between MP and ML, respectively. We selected 27 candidate genes for validation experiments using quantitative (Q-)PCR of genomic DNA. For tetraspanin TSPAN1, we studied mRNA expression levels in a separate cohort of primary breast carcinomas and in breast cell lines. RESULTS Matched primary (MP) tumors had a threefold higher rate of DNA copy number losses compared to UP tumors. In the UP-MP comparison, 186 BACs were differentially amplified or deleted. Most of them were localized to chromosomes 7p, 16q and 18q. In the MP-ML comparison, 131 BACs showed differential CNAs. Most of them were localized to chromosomes 1q and 20. By Q-PCR, seven candidate genes could be confirmed to show differential distributions of CNAs. TSPAN1 was amplified in UP and deleted in MP tumors. The gene was markedly downregulated in ER-negative and high-grade breast cancers. CONCLUSIONS Metastasizing tumors had a higher rate of deletions, suggesting possible inactivation of metastasis suppressor genes. We provide preliminary evidence that TSPAN1 may be another important breast cancer suppressor gene belonging to the tetraspanin superfamily.
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Affiliation(s)
- Mohamed M Desouki
- Department of Pathology, Medical University of South Carolina, Charleston, SC 29425, USA
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19
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Amplification of the prolactin receptor gene in mammary lobular neoplasia. Breast Cancer Res Treat 2010; 128:31-40. [PMID: 20658264 DOI: 10.1007/s10549-010-1025-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Accepted: 06/29/2010] [Indexed: 12/31/2022]
Abstract
The identification of lobular carcinoma in situ (LCIS) in a patient's specimen confers an appreciable increased risk of development of future invasive mammary carcinoma. However, the study of LCIS presents a challenge as it is usually only recognized in fixed specimens. Recent advances in high throughput genomics have made possible comprehensive copy number analysis of lesions such as this. Using array comparative genomic hybridization (aCGH), we characterized eight cases of lobular carcinoma (four invasive and four non-invasive) from microdissected samples of archival specimens and validated our results by quantitative real-time PCR (qRT-PCR). Immunohistochemistry (IHC) was performed on an independent set of 80 in situ ductal (DCIS) and lobular breast lesions to confirm our results. Amplification of the prolactin receptor gene (PRLr) was identified in 4/4 cases of LCIS by aCGH. We confirmed this amplification by qRT-PCR and demonstrated PRLr expression in 29/40 (73%) cases of lobular neoplasia by IHC. Amplification of PRLr was neither detected in 10 cases of DCIS nor in 5 areas of normal breast tissue by qRT-PCR and only 14/40 (35%) cases of DCIS showed PRLr expression by IHC (P = 0.0008). Our study suggests the prolactin receptor gene is a molecular target that may be important in the pathogenesis and progression of lobular neoplasia. Investigation of the status of this gene in cases of DCIS has indicated that it may not be as important in the progression of this type of breast cancer, supporting the view that lobular and ductal carcinomas may evolve along separate pathways.
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