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Zhang Q, Nong Y, Liu Z, Gong L. Proteinase K Combining Two-Step Liquid–Liquid Extraction for Plasma Untargeted Liquid Chromatography–Mass Spectrometry-Based Metabolomics To Discover the Potential Mechanism of Colorectal Adenoma. Anal Chem 2019; 91:14458-14466. [DOI: 10.1021/acs.analchem.9b03121] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Qisong Zhang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, People’s Republic of China
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Yanying Nong
- Guangdong Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, People’s Republic of China
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, People’s Republic of China
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Lingzhi Gong
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, People’s Republic of China
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, People’s Republic of China
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Ford KL, Anwar M, Heys R, Ahmed EM, Caputo M, Game L, Reeves BC, Punjabi PP, Angelini GD, Petretto E, Emanueli C. Optimisation of laboratory methods for whole transcriptomic RNA analyses in human left ventricular biopsies and blood samples of clinical relevance. PLoS One 2019; 14:e0213685. [PMID: 30870483 PMCID: PMC6417664 DOI: 10.1371/journal.pone.0213685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/18/2019] [Indexed: 01/08/2023] Open
Abstract
This study aimed to optimise techniques for whole transcriptome and small RNA analyses on clinical tissue samples from patients with cardiovascular disease. Clinical samples often represent a particular challenge to extracting RNA of sufficient quality for robust RNA sequencing analysis, and due to availability, it is rarely possible to optimise techniques on the samples themselves. Therefore, we have used equivalent samples from pigs undergoing cardiopulmonary bypass surgery to test different protocols for optimal RNA extraction, and then validated the protocols in human samples. Here we present an assessment of the quality and quantity of RNA obtained using a variety of commercially-available RNA extraction kits on both left ventricular biopsies and blood plasma. RNA extraction from these samples presents different difficulties; left ventricular biopsies are small and fibrous, while blood plasma has a low RNA content. We have validated our optimised extraction techniques on human clinical samples collected as part of the ARCADIA (Association of non-coding RNAs with Coronary Artery Disease and type 2 Diabetes) cohort study, resulting in successful whole transcriptome and small RNA sequencing of human left ventricular tissue.
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Affiliation(s)
- Kerrie L. Ford
- National Heart and Lung Institute, ICTEM, The Hammersmith Hospital, Imperial College London, London, United Kingdom
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Maryam Anwar
- National Heart and Lung Institute, ICTEM, The Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Rachael Heys
- Clinical Trials and Evaluation Unit, Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Eltayeb Mohamed Ahmed
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Massimo Caputo
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
- University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Laurence Game
- MRC London Institute of Medical Sciences, The Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Barnaby C. Reeves
- Clinical Trials and Evaluation Unit, Bristol Trials Centre, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Prakash P. Punjabi
- National Heart and Lung Institute, ICTEM, The Hammersmith Hospital, Imperial College London, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Gianni D. Angelini
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
- University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Enrico Petretto
- MRC London Institute of Medical Sciences, The Hammersmith Hospital, Imperial College London, London, United Kingdom
- Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Costanza Emanueli
- National Heart and Lung Institute, ICTEM, The Hammersmith Hospital, Imperial College London, London, United Kingdom
- Bristol Heart Institute, School of Translational Health Sciences, University of Bristol, Bristol, United Kingdom
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Dale TP, Forsyth NR. Ectopic Telomerase Expression Fails to Maintain Chondrogenic Capacity in Three-Dimensional Cultures of Clinically Relevant Cell Types. Biores Open Access 2018; 7:10-24. [PMID: 29588876 PMCID: PMC5865620 DOI: 10.1089/biores.2018.0008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The poor healing capacity of cartilage and lack of effective treatment for associated disease and trauma makes it a strong candidate for a regenerative medicine approach. Potential therapies tested to date, although effective, have met with a number of intrinsic difficulties possibly related to limited autologous chondrocyte cell yield and quality of cartilage produced. A potential mechanism to bypass limited cell yields and improve quality of differentiation is to immortalize relevant cell types through the ectopic expression of telomerase. Pellet cultures of human chondrocytes (OK3), bone marrow mesenchymal stem cells (BMA13), and embryonic stem cell (H1 line)-derived cells (1C6) and their human telomerase reverse transcriptase (hTERT) transduced counterparts were maintained for 20 days in standard maintenance medium (MM) or transforming growth factor-β3-supplemented prochondrogenic medium (PChM). Pellets were assessed for volume and density by microcomputed tomography. Quantitative gene expression (COL1A2, COL2A1, COL3A1, COL6A3, COL10A1, ACAN, COMP, SOX9); sulfated glycosaminoglycans (sGAGs), and DNA quantification were performed. Histology and immunohistochemistry were used to determine matrix constituent distribution. Pellet culture in PChM resulted in significantly larger pellets with an overall increased density when compared with MM culture. Gene expression analysis revealed similarities in expression patterns between telomerase-transduced and parental cells in both MM and PChM. Of the three parental cell types examined OK3 and BMA13 produced similar amounts of pellet-associated sGAG in PChM (4.62 ± 1.20 and 4.91 ± 1.37 μg, respectively) with lower amounts in 1C6 (2.89 ± 0.52 μg), corresponding to 3.1, 2.3, and 1.6-fold increases from day 0. In comparison, telomerase-transduced cells all had much lower sGAG with OK3H at 2.74 ± 0.11 μg, BMA13H 1.29 ± 0.34 μg, and 1C6H 0.52 ± 0.01 μg corresponding to 1.2, 0.87, and 0.34-fold changes compared with day 0. Histology of day 20 pellets displayed reduced staining overall for collagens and sGAG in telomerase-transduced cells, most notably with alterations in aggrecan and collagen VI; all cells stained positively for collagen II. We conclude that while telomerase transduction may be an effective technique to extend cellular proliferative capacity, it is not sufficient in isolation to sustain a naive chondrogenic phenotype across multiple cell types.
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Affiliation(s)
- Tina P Dale
- Faculty of Medicine and Health Sciences, Guy Hilton Research Center, Institute for Science and Technology in Medicine, Keele University, Staffordshire, United Kingdom
| | - Nicholas R Forsyth
- Faculty of Medicine and Health Sciences, Guy Hilton Research Center, Institute for Science and Technology in Medicine, Keele University, Staffordshire, United Kingdom
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Mao B, Moss CF, Wilkinson GS. Age-dependent gene expression in the inner ear of big brown bats (Eptesicus fuscus). PLoS One 2017; 12:e0186667. [PMID: 29073148 PMCID: PMC5658057 DOI: 10.1371/journal.pone.0186667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 10/05/2017] [Indexed: 12/25/2022] Open
Abstract
For echolocating bats, hearing is essential for survival. Specializations for detecting and processing high frequency sounds are apparent throughout their auditory systems. Recent studies on echolocating mammals have reported evidence of parallel evolution in some hearing-related genes in which distantly related groups of echolocating animals (bats and toothed whales), cluster together in gene trees due to apparent amino acid convergence. However, molecular adaptations can occur not only in coding sequences, but also in the regulation of gene expression. The aim of this study was to examine the expression of hearing-related genes in the inner ear of developing big brown bats, Eptesicus fuscus, during the period in which echolocation vocalizations increase dramatically in frequency. We found that seven genes were significantly upregulated in juveniles relative to adults, and that the expression of four genes through development correlated with estimated age. Compared to available data for mice, it appears that expression of some hearing genes is extended in juvenile bats. These results are consistent with a prolonged growth period required to develop larger cochlea relative to body size, a later maturation of high frequency hearing, and a greater dependence on high frequency hearing in echolocating bats.
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Affiliation(s)
- Beatrice Mao
- Department of Biology, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, Maryland, United States of America
| | - Cynthia F. Moss
- Department of Psychological and Brain Sciences, Zanvyl Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, Maryland, United States of America
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Gerald S. Wilkinson
- Department of Biology, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park, Maryland, United States of America
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Danielson KM, Rubio R, Abderazzaq F, Das S, Wang YE. High Throughput Sequencing of Extracellular RNA from Human Plasma. PLoS One 2017; 12:e0164644. [PMID: 28060806 PMCID: PMC5218574 DOI: 10.1371/journal.pone.0164644] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/28/2016] [Indexed: 01/03/2023] Open
Abstract
The presence and relative stability of extracellular RNAs (exRNAs) in biofluids has led to an emerging recognition of their promise as ‘liquid biopsies’ for diseases. Most prior studies on discovery of exRNAs as disease-specific biomarkers have focused on microRNAs (miRNAs) using technologies such as qRT-PCR and microarrays. The recent application of next-generation sequencing to discovery of exRNA biomarkers has revealed the presence of potential novel miRNAs as well as other RNA species such as tRNAs, snoRNAs, piRNAs and lncRNAs in biofluids. At the same time, the use of RNA sequencing for biofluids poses unique challenges, including low amounts of input RNAs, the presence of exRNAs in different compartments with varying degrees of vulnerability to isolation techniques, and the high abundance of specific RNA species (thereby limiting the sensitivity of detection of less abundant species). Moreover, discovery in human diseases often relies on archival biospecimens of varying age and limiting amounts of samples. In this study, we have tested RNA isolation methods to optimize profiling exRNAs by RNA sequencing in individuals without any known diseases. Our findings are consistent with other recent studies that detect microRNAs and ribosomal RNAs as the major exRNA species in plasma. Similar to other recent studies, we found that the landscape of biofluid microRNA transcriptome is dominated by several abundant microRNAs that appear to comprise conserved extracellular miRNAs. There is reasonable correlation of sets of conserved miRNAs across biological replicates, and even across other data sets obtained at different investigative sites. Conversely, the detection of less abundant miRNAs is far more dependent on the exact methodology of RNA isolation and profiling. This study highlights the challenges in detecting and quantifying less abundant plasma miRNAs in health and disease using RNA sequencing platforms.
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Affiliation(s)
- Kirsty M. Danielson
- Cardiovascular Institute, Massachusetts General Hospital, Boston, MA, United States of America
| | - Renee Rubio
- Center for Cancer Computational Biology, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, United States of America
| | - Fieda Abderazzaq
- Center for Cancer Computational Biology, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, United States of America
| | - Saumya Das
- Cardiovascular Institute, Massachusetts General Hospital, Boston, MA, United States of America
- * E-mail: (YEW); (SD)
| | - Yaoyu E. Wang
- Center for Cancer Computational Biology, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, United States of America
- * E-mail: (YEW); (SD)
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Criscione SW, Theodosakis N, Micevic G, Cornish TC, Burns KH, Neretti N, Rodić N. Genome-wide characterization of human L1 antisense promoter-driven transcripts. BMC Genomics 2016; 17:463. [PMID: 27301971 PMCID: PMC4908685 DOI: 10.1186/s12864-016-2800-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/26/2016] [Indexed: 11/23/2022] Open
Abstract
Background Long INterspersed Element-1 (LINE-1 or L1) is the only autonomously active, transposable element in the human genome. L1 sequences comprise approximately 17 % of the human genome, but only the evolutionarily recent, human-specific subfamily is retrotransposition competent. The L1 promoter has a bidirectional orientation containing a sense promoter that drives the transcription of two proteins required for retrotransposition and an antisense promoter. The L1 antisense promoter can drive transcription of chimeric transcripts: 5’ L1 antisense sequences spliced to the exons of neighboring genes. Results The impact of L1 antisense promoter activity on cellular transcriptomes is poorly understood. To investigate this, we analyzed GenBank ESTs for messenger RNAs that initiate in the L1 antisense promoter. We identified 988 putative L1 antisense chimeric transcripts, 911 of which have not been previously reported. These appear to be alternative genic transcripts, sense-oriented with respect to gene and initiating near, but typically downstream of, the gene transcriptional start site. In multiple cell lines, L1 antisense promoters display enrichment for YY1 transcription factor and histone modifications associated with active promoters. Global run-on sequencing data support the activity of the L1 antisense promoter. We independently detected 124 L1 antisense chimeric transcripts using long read Pacific Biosciences RNA-seq data. Furthermore, we validated four chimeric transcripts by quantitative RT-PCR and Sanger sequencing and demonstrated that they are readily detectable in many normal human tissues. Conclusions We present a comprehensive characterization of human L1 antisense promoter-driven transcripts and provide substantial evidence that they are transcribed in a variety of human cell-types. Our findings reveal a new wide-reaching aspect of L1 biology by identifying antisense transcripts affecting as many as 4 % of all human genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2800-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Steven W Criscione
- Department of Molecular Biology, Cell Biology, and Biochemistry, Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA
| | - Nicholas Theodosakis
- Department of Pathology, Yale University, New Haven, CT, 06510, USA.,Department of Dermatology, Division of Dermatopathology, Yale University, New Haven, CT, 06510, USA
| | - Goran Micevic
- Department of Pathology, Yale University, New Haven, CT, 06510, USA.,Department of Dermatology, Division of Dermatopathology, Yale University, New Haven, CT, 06510, USA
| | - Toby C Cornish
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,High Throughput (HiT) Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology, and Biochemistry, Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA.
| | - Nemanja Rodić
- Department of Pathology, Yale University, New Haven, CT, 06510, USA. .,Department of Dermatology, Division of Dermatopathology, Yale University, New Haven, CT, 06510, USA.
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Foukakis T, Lövrot J, Sandqvist P, Xie H, Lindström LS, Giorgetti C, Jacobsson H, Hedayati E, Bergh J. Gene expression profiling of sequential metastatic biopsies for biomarker discovery in breast cancer. Mol Oncol 2015; 9:1384-91. [PMID: 25888067 DOI: 10.1016/j.molonc.2015.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 03/10/2015] [Accepted: 03/23/2015] [Indexed: 11/17/2022] Open
Abstract
The feasibility of longitudinal metastatic biopsies for gene expression profiling in breast cancer is unexplored. Dynamic changes in gene expression can potentially predict efficacy of targeted cancer drugs. Patients enrolled in a phase III trial of metastatic breast cancer with docetaxel monotherapy versus combination of docetaxel + sunitinib were offered to participate in a translational substudy comprising longitudinal fine needle aspiration biopsies and Positron Emission Tomography imaging before (T1) and two weeks after start of treatment (T2). Aspirated tumor material was used for microarray analysis, and treatment-induced changes (T2 versus T1) in gene expression and standardized uptake values (SUV) were investigated and correlated to clinical outcome measures. Gene expression profiling yielded high-quality data at both time points in 14/18 patients. Unsupervised clustering revealed specific patterns of changes caused by monotherapy vs. combination therapy (p = 0.021, Fisher's exact test). A therapy-induced reduction of known proliferation and hypoxia metagene scores was prominent in the combination arm. Changes in a previously reported hypoxia metagene score were strongly correlated to the objective responses seen by conventional radiology assessments after 6 weeks in the combination arm, Spearman's ρ = 1 (p = 0.017) but not in monotherapy, ρ = -0.029 (p = 1). Similarly, the Predictor Analysis of Microarrays 50 (PAM50) proliferation metagene correlated to tumor changes merely in the combination arm at 6 and 12 weeks (ρ = 0.900, p = 0.083 and ρ = 1, p = 0.017 respectively). Reductions in mean SUV were a reliable early predictor of objective response in monotherapy, ρ = 0.833 (p = 0.008), but not in the combination arm ρ = -0.029 (p = 1). Gene expression profiling of longitudinal metastatic aspiration biopsies was feasible, demonstrated biological validity and provided predictive information.
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Affiliation(s)
- Theodoros Foukakis
- Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden.
| | - John Lövrot
- Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Patricia Sandqvist
- Department of Radiology and Nuclear Medicine, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Hanjing Xie
- Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Linda S Lindström
- Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Department of Surgery, University of California at San Francisco, USA
| | | | - Hans Jacobsson
- Department of Radiology and Nuclear Medicine, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Elham Hedayati
- Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Jonas Bergh
- Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden
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D'Apice L, Costa V, Valente C, Trovato M, Pagani A, Manera S, Regolo L, Zambelli A, Ciccodicola A, De Berardinis P. Analysis of SEMA6B gene expression in breast cancer: Identification of a new isoform. Biochim Biophys Acta Gen Subj 2013; 1830:4543-53. [DOI: 10.1016/j.bbagen.2013.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/29/2013] [Accepted: 05/01/2013] [Indexed: 01/04/2023]
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Caetano-Lopes J, Rodrigues A, Lopes A, Vale AC, Pitts-Kiefer MA, Vidal B, Perpétuo IP, Monteiro J, Konttinen YT, Vaz MF, Nazarian A, Canhão H, Fonseca JE. Rheumatoid Arthritis Bone Fragility Is Associated With Upregulation of IL17 and DKK1 Gene Expression. Clin Rev Allergy Immunol 2013; 47:38-45. [DOI: 10.1007/s12016-013-8366-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Rodrigues AM, Caetano-Lopes J, Vale AC, Vidal B, Lopes A, Aleixo I, Polido-Pereira J, Sepriano A, Perpétuo IP, Monteiro J, Vaz MF, Fonseca JE, Canhão H. Low osteocalcin/collagen type I bone gene expression ratio is associated with hip fragility fractures. Bone 2012; 51:981-9. [PMID: 22975110 DOI: 10.1016/j.bone.2012.08.129] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Revised: 07/27/2012] [Accepted: 08/25/2012] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Osteocalcin (OC) is the most abundant non-collagenous bone protein and is determinant for bone mineralization. We aimed to compare OC bone expression and serum factors related to its carboxylation in hip fragility fracture and osteoarthritis patients. We also aimed to identify which of these factors were associated with worse mechanical behavior and with the hip fracture event. METHODS In this case-control study, fragility fracture patients submitted to hip replacement surgery were evaluated and compared to a group of osteoarthritis patients submitted to the same procedure. Fasting blood samples were collected to assess apolipoproteinE (apoE) levels, total OC and undercarboxylated osteocalcin (ucOC), vitamin K, LDL cholesterol, triglycerides and bone turnover markers. The frequency of the apoε4 isoform was determined. Femoral epiphyses were collected and trabecular bone cylinders drilled in order to perform compression mechanical tests. Gene expression of bone matrix components was assessed by quantitative RT-PCR analysis. RESULTS 64 patients, 25 submitted to hip replacement surgery due to fragility fracture and 39 due to osteoarthritis, were evaluated. Bone OC/collagen expression (OC/COL1A1) ratio was significantly lower in hip fracture compared to osteoarthritis patients (p<0.017) adjusted for age, gender and body mass index. Moreover, OC/COL1A1 expression ratio was associated with the hip fracture event (OR ~0; p=0.003) independently of the group assigned, or the clinical characteristics. Apoε4 isoform was more frequent in the hip fracture group (p=0.029). ucOC levels were higher in the fracture group although not significantly (p=0.058). No differences were found regarding total OC (p=0.602), apoE (p=0.467) and Vitamin K (p=0.371). In hip fracture patients, multivariate analysis, adjusted for clinical characteristics, serum factors related to OC metabolism and gene expression of bone matrix proteins showed that low OC/COL1A1 expression ratio was significantly associated with worse trabecular strength (β=0.607; p=0.013) and stiffness (β=0.693; p=0.003). No association was found between ucOC and bone mechanics. Moreover, in osteoarthritis patients, the multivariate analysis revealed that serum total OC was negatively associated with strength (β=-0.411; p=0.030) and stiffness (β=-0.487; p=0.009). CONCLUSION We demonstrated that low bone OC/COL1A1 expression ratio was an independent predictor of worse trabecular mechanical behavior and of the hip fracture event. These findings suggest that in hip fracture patients the imbalance of bone OC/COL1A1 expression ratio reflects disturbances in osteoblast activity leading to bone fragility.
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Affiliation(s)
- Ana M Rodrigues
- Rheumatology Research Unit, Instituto de Medicina Molecular, Lisbon, Portugal.
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Evaluation of microRNA expression in patient bone marrow aspirate slides. PLoS One 2012; 7:e42951. [PMID: 22912766 PMCID: PMC3418238 DOI: 10.1371/journal.pone.0042951] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Accepted: 07/16/2012] [Indexed: 11/19/2022] Open
Abstract
Like formalin fixed paraffin embedded (FFPE) tissues, archived bone marrow aspirate slides are an abundant and untapped resource of biospecimens that could enable retrospective molecular studies of disease. Historically, RNA obtained from slides is limited in utility because of their low quality and highly fragmented nature. MicroRNAs are small (≈22 nt) non-coding RNA that regulate gene expression, and are speculated to preserve well in FFPE tissue. Here we investigate the use of archived bone marrow aspirate slides for miRNA expression analysis in paediatric leukaemia. After determining the optimal method of miRNA extraction, we used TaqMan qRT-PCR to identify reference miRNA for normalisation of other miRNA species. We found hsa-miR-16 and hsa-miR-26b to be the most stably expressed between lymphoblastoid cell lines, primary bone marrow aspirates and archived samples. We found the average fold change in expression of hsa-miR-26b and two miRNA reportedly dysregulated in leukaemia (hsa-miR-128a, hsa-miR-223) was <0.5 between matching archived slide and bone marrow aspirates. Differential expression of hsa-miR-128a and hsa-miR-223 was observed between leukaemic and non-leukaemic bone marrow from archived slides or flash frozen bone marrow. The demonstration that archived bone marrow aspirate slides can be utilized for miRNA expression studies offers tremendous potential for future investigations into the role miRNA play in the development and long term outcome of hematologic, as well as non-hematologic, diseases.
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Caetano-Lopes J, Lopes A, Rodrigues A, Fernandes D, Perpétuo IP, Monjardino T, Lucas R, Monteiro J, Konttinen YT, Canhão H, Fonseca JE. Upregulation of inflammatory genes and downregulation of sclerostin gene expression are key elements in the early phase of fragility fracture healing. PLoS One 2011; 6:e16947. [PMID: 21347301 PMCID: PMC3037947 DOI: 10.1371/journal.pone.0016947] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Accepted: 01/18/2011] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Fracture healing is orchestrated by a specific set of events that culminates in the repair of bone and reachievement of its biomechanical properties. The aim of our work was to study the sequence of gene expression events involved in inflammation and bone remodeling occurring in the early phases of callus formation in osteoporotic patients. METHODOLOGY/PRINCIPAL FINDINGS Fifty-six patients submitted to hip replacement surgery after a low-energy hip fracture were enrolled in this study. The patients were grouped according to the time interval between fracture and surgery: bone collected within 3 days after fracture (n = 13); between the 4(th) and 7(th) day (n = 33); and after one week from the fracture (n = 10). Inflammation- and bone metabolism-related genes were assessed at the fracture site. The expression of pro-inflammatory cytokines was increased in the first days after fracture. The genes responsible for bone formation and resorption were upregulated one week after fracture. The increase in RANKL expression occurred just before that, between the 4(th)-7(th) days after fracture. Sclerostin expression diminished during the first days after fracture. CONCLUSIONS The expression of inflammation-related genes, especially IL-6, is highest at the very first days after fracture but from day 4 onwards there is a shift towards bone remodeling genes, suggesting that the inflammatory phase triggers bone healing. We propose that an initial inflammatory stimulus and a decrease in sclerostin-related effects are the key components in fracture healing. In osteoporotic patients, cellular machinery seems to adequately react to the inflammatory stimulus, therefore local promotion of these events might constitute a promising medical intervention to accelerate fracture healing.
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Affiliation(s)
- Joana Caetano-Lopes
- Rheumatology Research Unit, Faculdade de Medicina da Universidade de Lisboa, Instituto de Medicina Molecular, Lisbon, Portugal
| | - Ana Lopes
- Rheumatology Research Unit, Faculdade de Medicina da Universidade de Lisboa, Instituto de Medicina Molecular, Lisbon, Portugal
| | - Ana Rodrigues
- Rheumatology Research Unit, Faculdade de Medicina da Universidade de Lisboa, Instituto de Medicina Molecular, Lisbon, Portugal
- Serviço de Reumatologia e Doenças Ósseas Metabólicas, Hospital de Santa Maria, Lisbon, Portugal
| | - Diana Fernandes
- Rheumatology Research Unit, Faculdade de Medicina da Universidade de Lisboa, Instituto de Medicina Molecular, Lisbon, Portugal
| | - Inês P. Perpétuo
- Rheumatology Research Unit, Faculdade de Medicina da Universidade de Lisboa, Instituto de Medicina Molecular, Lisbon, Portugal
| | - Teresa Monjardino
- Department of Hygiene and Epidemiology, University of Porto Medical School, Porto, Portugal
- Institute of Public Health, University of Porto, Porto, Portugal
| | - Raquel Lucas
- Department of Hygiene and Epidemiology, University of Porto Medical School, Porto, Portugal
- Institute of Public Health, University of Porto, Porto, Portugal
| | - Jacinto Monteiro
- Orthopaedics Department, Hospital de Santa Maria, Lisbon, Portugal
| | - Yrjö T. Konttinen
- Department of Medicine, University of Helsinki, Helsinki, Finland
- ORTON Orthopaedic Hospital of the Invalid Foundation, Helsinki, Finland
- COXA Hospital for Joint Replacement, Tampere, Finland
| | - Helena Canhão
- Rheumatology Research Unit, Faculdade de Medicina da Universidade de Lisboa, Instituto de Medicina Molecular, Lisbon, Portugal
- Serviço de Reumatologia e Doenças Ósseas Metabólicas, Hospital de Santa Maria, Lisbon, Portugal
| | - João E. Fonseca
- Rheumatology Research Unit, Faculdade de Medicina da Universidade de Lisboa, Instituto de Medicina Molecular, Lisbon, Portugal
- Serviço de Reumatologia e Doenças Ósseas Metabólicas, Hospital de Santa Maria, Lisbon, Portugal
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Vestergaard AL, Knudsen UB, Munk T, Rosbach H, Martensen PM. Transcriptional expression of type-I interferon response genes and stability of housekeeping genes in the human endometrium and endometriosis. Mol Hum Reprod 2010; 17:243-54. [PMID: 21156832 DOI: 10.1093/molehr/gaq100] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Endometriosis is a painful chronic female disease defined by the presence of endometrial tissue implants in ectopic (Ec) locations. The pathogenesis is much debated, and type-I interferons (IFNs) could be involved. The expression of genes of the type-I IFN response were profiled by a specific PCR array of RNA obtained from Ec and eutopic (Eu) endometrium collected from nine endometriosis patients and nine healthy control women. Transcriptional expression levels of selected IFN-regulated and housekeeping genes (HKGs) were investigated by real-time quantitative reverse transcriptase PCR (qRT-PCR). Stably expressed HKGs for valid normalization of transcriptional studies of endometrium and endometriosis have not yet been published. Here, seven HKGs were evaluated for stability using the GeNorm and NormFinder software. A normalization factor based on HMBS, TBP and YWHAZ expression was suitable for normalization of qRT-PCR studies of Eu versus Ec endometrium. In the endometrial cell lines HEC1A, HEC1B, Ishikawa and RL95-2, HMBS and HPRT1 were the most stably expressed. The IFN-specific PCR array indicated significantly different expression of the genes BST2, COL16A1, HOXB2 and ISG20 between the endometrial tissue types. However, by correctly normalized qRT-PCR, levels of BST2, COL16A1 and the highly type-I IFN-stimulated genes ISG12A and 6-16 displayed insignificant variations. Conversely, HOXB2 and ISG20 transcriptions were significantly reduced in endometriosis lesions compared with endometrium from endometriosis patients and healthy controls. In conclusion, appropriate HKGs for normalization of qRT-PCR studies of endometrium and endometriosis have been identified here. Abolished expression of ISG20 and HOX genes could be important in endometriosis.
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Affiliation(s)
- Anna L Vestergaard
- Department of Molecular Biology, Aarhus University, 8000 Aarhus C, Denmark
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Larionov AA, Miller WR. Challenges in defining predictive markers for response to endocrine therapy in breast cancer. Future Oncol 2010; 5:1415-28. [PMID: 19903069 DOI: 10.2217/fon.09.113] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Endocrine therapy is a major treatment modality for hormone-dependent breast cancer. It has a relatively low morbidity, and there is evidence that antihormonal treatments have had a significant effect in reducing mortality for breast cancer. Despite this, resistance to endocrine therapy, either primary or acquired during treatment, occurs in the majority of patients, and is a major obstacle to optimal clinical management. There is therefore an urgent need to identify, on an individual basis, those tumors that are most likely to respond to endocrine therapy (so sparing patients with resistant tumors the needless side effects of ineffective therapy), and the mechanisms of resistance in tumors that are nonresponsive to treatment (so these can be bypassed). These needs are the focus of this review, which discusses the particular issues encountered when investigating the potential of multigene expression signatures as predictive factors for response to aromatase inhibitors, which have recently become front-line endocrine therapies for postmenopausal patients with breast cancer.
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Affiliation(s)
- Alexey A Larionov
- Edinburgh Breakthrough Breast Research Unit, University of Edinburgh, Edinburgh, UK
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15
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Dumur CI, Lyons-Weiler M, Sciulli C, Garrett CT, Schrijver I, Holley TK, Rodriguez-Paris J, Pollack JR, Zehnder JL, Price M, Hagenkord JM, Rigl CT, Buturovic LJ, Anderson GG, Monzon FA. Interlaboratory performance of a microarray-based gene expression test to determine tissue of origin in poorly differentiated and undifferentiated cancers. J Mol Diagn 2008; 10:67-77. [PMID: 18083688 PMCID: PMC2175545 DOI: 10.2353/jmoldx.2008.070099] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2007] [Indexed: 02/02/2023] Open
Abstract
Clinical workup of metastatic malignancies of unknown origin is often arduous and expensive and is reported to be unsuccessful in 30 to 60% of cases. Accurate classification of uncertain primary cancers may improve with microarray-based gene expression testing. We evaluated the analytical performance characteristics of the Pathwork tissue of origin test, which uses expression signals from 1668 probe sets in a gene expression microarray, to quantify the similarity of tumor specimens to 15 known tissues of origin. Sixty archived tissue specimens from poorly and undifferentiated tumors (metastatic and primary) were analyzed at four laboratories representing a wide range of preanalytical conditions (eg, personnel, reagents, instrumentation, and protocols). Cross-laboratory comparisons showed highly reproducible results between laboratories, with correlation coefficients between 0.95 to 0.97 for measurements of similarity scores, and an average 93.8% overall concordance between laboratories in terms of final tissue calls. Bland-Altman plots (mean coefficients of reproducibility of 32.48+/-3.97) and kappa statistics (kappa >0.86) also indicated a high level of agreement between laboratories. We conclude that the Pathwork tissue of origin test is a robust assay that produces consistent results in diverse laboratory conditions reflecting the preanalytical variations found in the everyday clinical practice of molecular diagnostics laboratories.
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Affiliation(s)
- Catherine I. Dumur
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Maureen Lyons-Weiler
- Clinical Genomics Facility and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Christin Sciulli
- Clinical Genomics Facility and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Carleton T. Garrett
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Iris Schrijver
- Department of Pathology, Stanford University, Stanford, California
| | - Tara K. Holley
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | | | | | - James L. Zehnder
- Department of Pathology, Stanford University, Stanford, California
| | - Melissa Price
- Clinical Genomics Facility and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jill M. Hagenkord
- Clinical Genomics Facility and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | | | | | - Federico A. Monzon
- Clinical Genomics Facility and Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
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16
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Bergqvist J, Ohd JF, Smeds J, Klaar S, Isola J, Nordgren H, Elmberger GP, Hellborg H, Bjohle J, Borg AL, Skoog L, Bergh J. Quantitative real-time PCR analysis and microarray-based RNA expression of HER2 in relation to outcome. Ann Oncol 2007; 18:845-50. [PMID: 17351254 DOI: 10.1093/annonc/mdm059] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Our aim was to use quantitative real-time PCR (Q-PCR) and RNA expression profiles (RNA-EPs) to investigate HER2 status in relation to outcome. PATIENTS AND METHODS Cut-off levels for Q-PCR and RNA-EP were established in relation to immunohistochemistry (IHC) validated by FISH in a test set of frozen tissue samples from 40 primary breast cancers. The HER2 status was subsequently studied in another validation set of 306 tumors, where Q-PCR and RNA-EP results were compared with previously carried out IHC that we had validated by chromogenic in situ hybridization (CISH). RESULTS Q-PCR and RNA-EP offered similar sensitivity (90% versus 77%), specificity (93% versus 95%), and negative (99% versus 98%) and positive (63% versus 61%) predictive values for HER2 determinations. Analyses of relapse-free survival (RFS) and overall survival on the basis of 5 and 10 years of follow-up indicated equivalent hazard ratios for all three techniques. In contrast to IHC/CISH, both Q-PCR and RNA-EP analyses of HER2 also gave statistically significant results regarding RFS and breast cancer-corrected survival after 10 years of follow-up. CONCLUSION The use of RNA-EP and Q-PCR to analyze HER2 in frozen and formalin-fixed breast cancer samples may be an alternate approach to IHC in combination with FISH/CISH.
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Affiliation(s)
- J Bergqvist
- Department of Oncology and Pathology, Karolinska Institute and University Hospital, Stockholm, Sweden.
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17
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Calza S, Hall P, Auer G, Bjöhle J, Klaar S, Kronenwett U, Liu ET, Miller L, Ploner A, Smeds J, Bergh J, Pawitan Y. Intrinsic molecular signature of breast cancer in a population-based cohort of 412 patients. Breast Cancer Res 2007; 8:R34. [PMID: 16846532 PMCID: PMC1779468 DOI: 10.1186/bcr1517] [Citation(s) in RCA: 196] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2006] [Revised: 05/02/2006] [Accepted: 06/21/2006] [Indexed: 11/10/2022] Open
Abstract
Background Molecular markers and the rich biological information they contain have great potential for cancer diagnosis, prognostication and therapy prediction. So far, however, they have not superseded routine histopathology and staging criteria, partly because the few studies performed on molecular subtyping have had little validation and limited clinical characterization. Methods We obtained gene expression and clinical data for 412 breast cancers obtained from population-based cohorts of patients from Stockholm and Uppsala, Sweden. Using the intrinsic set of approximately 500 genes derived in the Norway/Stanford breast cancer data, we validated the existence of five molecular subtypes – basal-like, ERBB2, luminal A/B and normal-like – and characterized these subtypes extensively with the use of conventional clinical variables. Results We found an overall 77.5% concordance between the centroid prediction of the Swedish cohort by using the Norway/Stanford signature and the k-means clustering performed internally within the Swedish cohort. The highest rate of discordant assignments occurred between the luminal A and luminal B subtypes and between the luminal B and ERBB2 subtypes. The subtypes varied significantly in terms of grade (p < 0.001), p53 mutation (p < 0.001) and genomic instability (p = 0.01), but surprisingly there was little difference in lymph-node metastasis (p = 0.31). Furthermore, current users of hormone-replacement therapy were strikingly over-represented in the normal-like subgroup (p < 0.001). Separate analyses of the patients who received endocrine therapy and those who did not receive any adjuvant therapy supported the previous hypothesis that the basal-like subtype responded to adjuvant treatment, whereas the ERBB2 and luminal B subtypes were poor responders. Conclusion We found that the intrinsic molecular subtypes of breast cancer are broadly present in a diverse collection of patients from a population-based cohort in Sweden. The intrinsic gene set, originally selected to reveal stable tumor characteristics, was shown to have a strong correlation with progression-related properties such as grade, p53 mutation and genomic instability.
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Affiliation(s)
- Stefano Calza
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobel väg 12A, SE-171 77 Stockholm, Sweden
- Section of Medical Statistics and Biometry, Department of Biotechnologies and Biomedical Sciences, Viale Europa 11, 25123 Brescia, University of Brescia, Italy
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobel väg 12A, SE-171 77 Stockholm, Sweden
| | - Gert Auer
- Department of Oncology and Pathology, Cancer Center Karolinska, Radiumhemmet, Karolinska Institutet and University Hospital, Solna SE-171 76 Stockholm, Sweden
| | - Judith Bjöhle
- Department of Oncology and Pathology, Cancer Center Karolinska, Radiumhemmet, Karolinska Institutet and University Hospital, Solna SE-171 76 Stockholm, Sweden
| | - Sigrid Klaar
- Department of Oncology and Pathology, Cancer Center Karolinska, Radiumhemmet, Karolinska Institutet and University Hospital, Solna SE-171 76 Stockholm, Sweden
| | - Ulrike Kronenwett
- Department of Oncology and Pathology, Cancer Center Karolinska, Radiumhemmet, Karolinska Institutet and University Hospital, Solna SE-171 76 Stockholm, Sweden
| | - Edison T Liu
- Genome Institute of Singapore, 60 Biopolis Street, #02-01, Genome, 138672 Singapore
| | - Lance Miller
- Genome Institute of Singapore, 60 Biopolis Street, #02-01, Genome, 138672 Singapore
| | - Alexander Ploner
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobel väg 12A, SE-171 77 Stockholm, Sweden
| | - Johanna Smeds
- Department of Oncology and Pathology, Cancer Center Karolinska, Radiumhemmet, Karolinska Institutet and University Hospital, Solna SE-171 76 Stockholm, Sweden
| | - Jonas Bergh
- Department of Oncology and Pathology, Cancer Center Karolinska, Radiumhemmet, Karolinska Institutet and University Hospital, Solna SE-171 76 Stockholm, Sweden
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobel väg 12A, SE-171 77 Stockholm, Sweden
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Abstract
DNA microarrays enable insights into global gene expression by capturing a snapshot of cellular expression levels at the time of sample collection. Careful RNA handling and extraction are required to preserve this information properly, ensure sample-to-sample reproducibility, and limit unwanted technical variation in experimental data. This chapter discusses important considerations for "array-friendly" sample handling and processing from biosamples such as blood, formalin-fixed, paraffin-embedded samples, and fresh or flash-frozen tissues and cells. It also provides guidelines on RNA quality assessments, which can be used to validate sample preparation and maximize recovery of relevant biological information.
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Hall P, Ploner A, Bjöhle J, Huang F, Lin CY, Liu ET, Miller LD, Nordgren H, Pawitan Y, Shaw P, Skoog L, Smeds J, Wedrén S, Öhd J, Bergh J. Hormone-replacement therapy influences gene expression profiles and is associated with breast-cancer prognosis: a cohort study. BMC Med 2006; 4:16. [PMID: 16813654 PMCID: PMC1555602 DOI: 10.1186/1741-7015-4-16] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 06/30/2006] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Postmenopausal hormone-replacement therapy (HRT) increases breast-cancer risk. The influence of HRT on the biology of the primary tumor, however, is not well understood. METHODS We obtained breast-cancer gene expression profiles using Affymetrix human genome U133A arrays. We examined the relationship between HRT-regulated gene profiles, tumor characteristics, and recurrence-free survival in 72 postmenopausal women. RESULTS HRT use in patients with estrogen receptor (ER) protein positive tumors (n = 72) was associated with an altered regulation of 276 genes. Expression profiles based on these genes clustered ER-positive tumors into two molecular subclasses, one of which was associated with HRT use and had significantly better recurrence free survival despite lower ER levels. A comparison with external data suggested that gene regulation in tumors associated with HRT was negatively correlated with gene regulation induced by short-term estrogen exposure, but positively correlated with the effect of tamoxifen. CONCLUSION Our findings suggest that post-menopausal HRT use is associated with a distinct gene expression profile related to better recurrence-free survival and lower ER protein levels. Tentatively, HRT-associated gene expression in tumors resembles the effect of tamoxifen exposure on MCF-7 cells.
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Affiliation(s)
- Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Ploner
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Judith Bjöhle
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and Hospital, Stockholm, Sweden
| | - Fei Huang
- Bristol-Myers Squibb, Princeton, NJ, USA
| | - Chin-Yo Lin
- Genome Institute of Singapore, Republic of Singapore
| | - Edison T Liu
- Genome Institute of Singapore, Republic of Singapore
| | | | - Hans Nordgren
- Department of Pathology, Uppsala University Hospital, Uppsala, Sweden
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter Shaw
- Bristol-Myers Squibb, Princeton, NJ, USA
| | - Lambert Skoog
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and Hospital, Stockholm, Sweden
| | - Johanna Smeds
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and Hospital, Stockholm, Sweden
| | - Sara Wedrén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - John Öhd
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and Hospital, Stockholm, Sweden
| | - Jonas Bergh
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and Hospital, Stockholm, Sweden
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20
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Pawitan Y, Bjöhle J, Amler L, Borg AL, Egyhazi S, Hall P, Han X, Holmberg L, Huang F, Klaar S, Liu ET, Miller L, Nordgren H, Ploner A, Sandelin K, Shaw PM, Smeds J, Skoog L, Wedrén S, Bergh J. Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res 2005; 7:R953-64. [PMID: 16280042 PMCID: PMC1410752 DOI: 10.1186/bcr1325] [Citation(s) in RCA: 582] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Revised: 08/19/2005] [Accepted: 09/02/2005] [Indexed: 11/17/2022] Open
Abstract
Introduction Adjuvant breast cancer therapy significantly improves survival, but overtreatment and undertreatment are major problems. Breast cancer expression profiling has so far mainly been used to identify women with a poor prognosis as candidates for adjuvant therapy but without demonstrated value for therapy prediction. Methods We obtained the gene expression profiles of 159 population-derived breast cancer patients, and used hierarchical clustering to identify the signature associated with prognosis and impact of adjuvant therapies, defined as distant metastasis or death within 5 years. Independent datasets of 76 treated population-derived Swedish patients, 135 untreated population-derived Swedish patients and 78 Dutch patients were used for validation. The inclusion and exclusion criteria for the studies of population-derived Swedish patients were defined. Results Among the 159 patients, a subset of 64 genes was found to give an optimal separation of patients with good and poor outcomes. Hierarchical clustering revealed three subgroups: patients who did well with therapy, patients who did well without therapy, and patients that failed to benefit from given therapy. The expression profile gave significantly better prognostication (odds ratio, 4.19; P = 0.007) (breast cancer end-points odds ratio, 10.64) compared with the Elston–Ellis histological grading (odds ratio of grade 2 vs 1 and grade 3 vs 1, 2.81 and 3.32 respectively; P = 0.24 and 0.16), tumor stage (odds ratio of stage 2 vs 1 and stage 3 vs 1, 1.11 and 1.28; P = 0.83 and 0.68) and age (odds ratio, 0.11; P = 0.55). The risk groups were consistent and validated in the independent Swedish and Dutch data sets used with 211 and 78 patients, respectively. Conclusion We have identified discriminatory gene expression signatures working both on untreated and systematically treated primary breast cancer patients with the potential to spare them from adjuvant therapy.
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Affiliation(s)
- Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Judith Bjöhle
- Department of Oncology and Pathology, Radiumhemmet, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | | | - Anna-Lena Borg
- Department of Oncology and Pathology, Radiumhemmet, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Suzanne Egyhazi
- Department of Oncology and Pathology, Radiumhemmet, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Xia Han
- Bristol-Myers Squibb, Princeton, New Jersey, USA
| | - Lars Holmberg
- Regional Oncological Center, Uppsala University Hospital, Uppsala, Sweden
| | - Fei Huang
- Bristol-Myers Squibb, Princeton, New Jersey, USA
| | - Sigrid Klaar
- Department of Oncology and Pathology, Radiumhemmet, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | | | | | - Hans Nordgren
- Department of Pathology, Uppsala University Hospital, Uppsala, Sweden
| | - Alexander Ploner
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Kerstin Sandelin
- Department of Surgery Sciences, Karolinska Institutet and Hospital, Stockholm, Sweden
| | - Peter M Shaw
- Bristol-Myers Squibb, Princeton, New Jersey, USA
| | - Johanna Smeds
- Department of Oncology and Pathology, Radiumhemmet, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Lambert Skoog
- Department of Oncology and Pathology, Radiumhemmet, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Sara Wedrén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jonas Bergh
- Department of Oncology and Pathology, Radiumhemmet, Karolinska Institutet and University Hospital, Stockholm, Sweden
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21
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Smeds J, Miller LD, Bjöhle J, Hall P, Klaar S, Liu ET, Pawitan Y, Ploner A, Bergh J. Gene profile and response to treatment. Ann Oncol 2005; 16 Suppl 2:ii195-202. [PMID: 15958456 DOI: 10.1093/annonc/mdi737] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- J Smeds
- Department of Oncology and Pathology, Radiumhemmet, Karolinska Institute and University Hospital, Stockholm, Sweden
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