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Torabi F, Vadakekolathu J, Wyatt R, Leete P, Tombs MA, Richardson CC, Boocock DJ, Turner MD, Morgan NG, Richardson SJ, Christie MR. Differential expression of genes controlling lymphocyte differentiation and migration in two distinct endotypes of type 1 diabetes. Diabet Med 2023; 40:e15155. [PMID: 37246834 DOI: 10.1111/dme.15155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/04/2023] [Accepted: 05/26/2023] [Indexed: 05/30/2023]
Abstract
AIMS Morphological studies of pancreas samples obtained from young people with recent-onset type 1 diabetes have revealed distinct patterns of immune cell infiltration of the pancreatic islets suggestive of two age-associated type 1 diabetes endotypes that differ by inflammatory responses and rates of disease progression. The objective of this study was to investigate whether these proposed disease endotypes are associated with pathological differences in immune cell activation and cytokine secretion by applying multiplexed gene expression analysis to pancreatic tissue from recent-onset type 1 diabetes cases. METHODS RNA was extracted from samples of fixed, paraffin-embedded pancreas tissue from type 1 diabetes cases characterised by endotype and from controls without diabetes. Expression levels of 750 genes associated with autoimmune inflammation were determined by hybridisation to a panel of capture and reporter probes and these were counted as a measure of gene expression. Normalised counts were analysed for differences in expression between 29 type 1 diabetes cases and 7 controls without diabetes, and between the two type 1 diabetes endotypes. RESULTS Ten inflammation-associated genes, including INS, were significantly under-expressed in both endotypes and 48 genes were more highly expressed. A different set of 13 genes associated with the development, activation and migration of lymphocytes was uniquely overexpressed in the pancreas of people developing diabetes at younger age. CONCLUSIONS The results provide evidence that histologically defined type 1 diabetes endotypes differ in their immunopathology and identify inflammatory pathways specifically involved in disease developing at a young age, essential for a better understanding of disease heterogeneity.
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Affiliation(s)
- Forough Torabi
- School of Life Sciences, University of Lincoln, Lincoln, UK
| | | | - Rebecca Wyatt
- Islet Biology Exeter (IBEx), Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Pia Leete
- Islet Biology Exeter (IBEx), Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | | | | | - David J Boocock
- John van Geest Cancer Research Centre, Nottingham Trent University, Nottingham, UK
| | - Mark D Turner
- Centre for Diabetes, Chronic Diseases and Ageing, Nottingham Trent University, Nottingham, UK
| | - Noel G Morgan
- Islet Biology Exeter (IBEx), Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Sarah J Richardson
- Islet Biology Exeter (IBEx), Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
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2
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Cerri F, Gentile F, Clarelli F, Santoro S, Falzone YM, Dina G, Romano A, Domi T, Pozzi L, Fazio R, Podini P, Sorosina M, Carrera P, Esposito F, Riva N, Briani C, Cavallaro T, Filippi M, Quattrini A. Clinical and pathological findings in neurolymphomatosis: Preliminary association with gene expression profiles in sural nerves. Front Oncol 2022; 12:974751. [PMID: 36226068 PMCID: PMC9549065 DOI: 10.3389/fonc.2022.974751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Although inflammation appears to play a role in neurolymphomatosis (NL), the mechanisms leading to degeneration in the peripheral nervous system are poorly understood. The purpose of this exploratory study was to identify molecular pathways underlying NL pathogenesis, combining clinical and neuropathological investigation with gene expression (GE) studies. We characterized the clinical and pathological features of eight patients with NL. We further analysed GE changes in sural nerve biopsies obtained from a subgroup of NL patients (n=3) and thirteen patients with inflammatory neuropathies as neuropathic controls. Based on the neuropathic symptoms and signs, NL patients were classified into three forms of neuropathy: chronic symmetrical sensorimotor polyneuropathy (SMPN, n=3), multiple mononeuropathy (MN, n=4) and acute motor-sensory axonal neuropathy (AMSAN, n=1). Predominantly diffuse malignant cells infiltration of epineurium was present in chronic SMPN, whereas endoneurial perivascular cells invasion was observed in MN. In contrast, diffuse endoneurium malignant cells localization occurred in AMSAN. We identified alterations in the expression of 1266 genes, with 115 up-regulated and 1151 down-regulated genes, which were mainly associated with ribosomal proteins (RP) and olfactory receptors (OR) signaling pathways, respectively. Among the top up-regulated genes were actin alpha 1 skeletal muscle (ACTA1) and desmin (DES). Similarly, in NL nerves ACTA1, DES and several RPs were highly expressed, associated with endothelial cells and pericytes abnormalities. Peripheral nerve involvement may be due to conversion towards a more aggressive phenotype, potentially explaining the poor prognosis. The candidate genes reported in this study may be a source of clinical biomarkers for NL.
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Affiliation(s)
- Federica Cerri
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Gentile
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Ferdinando Clarelli
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Santoro
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Yuri Matteo Falzone
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Giorgia Dina
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Romano
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Teuta Domi
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Laura Pozzi
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Raffaella Fazio
- Department of Neurology, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Paola Podini
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Melissa Sorosina
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Paola Carrera
- Division of Genetics and Cell Biology and Laboratory of Clinical Molecular Biology and Cytogenetics, Unit of Genomics for Human Disease Diagnosis, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Federica Esposito
- Department of Neurology, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Nilo Riva
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- *Correspondence: Nilo Riva, ; Angelo Quattrini,
| | - Chiara Briani
- Department of Neuroscience , University of Padova, Padova, Italy
| | - Tiziana Cavallaro
- Department of Neurology, Azienda Ospedaliera Universitaria Integrata, University Hospital G.B. Rossi, Verona, Italy
| | - Massimo Filippi
- Department of Neurology, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Angelo Quattrini
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- *Correspondence: Nilo Riva, ; Angelo Quattrini,
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Piyawajanusorn C, Nguyen LC, Ghislat G, Ballester PJ. A gentle introduction to understanding preclinical data for cancer pharmaco-omic modeling. Brief Bioinform 2021; 22:6343527. [PMID: 34368843 DOI: 10.1093/bib/bbab312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/25/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022] Open
Abstract
A central goal of precision oncology is to administer an optimal drug treatment to each cancer patient. A common preclinical approach to tackle this problem has been to characterize the tumors of patients at the molecular and drug response levels, and employ the resulting datasets for predictive in silico modeling (mostly using machine learning). Understanding how and why the different variants of these datasets are generated is an important component of this process. This review focuses on providing such introduction aimed at scientists with little previous exposure to this research area.
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Affiliation(s)
- Chayanit Piyawajanusorn
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France.,Faculty of Medicine and Public Health, HRH Princess Chulabhorn College of Medical Science, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Linh C Nguyen
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France.,Department of Life Sciences, University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ghita Ghislat
- U1104, CNRS UMR7280, Centre d'Immunologie de Marseille-Luminy, Inserm, Marseille, France
| | - Pedro J Ballester
- Cancer Research Center of Marseille, INSERM U1068, F-13009 Marseille, France.,Institut Paoli-Calmettes, F-13009 Marseille, France.,Aix-Marseille Université, F-13284 Marseille, France.,CNRS UMR7258, F-13009 Marseille, France
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4
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An Integrated Transcriptomic Approach to Identify Molecular Markers of Calcineurin Inhibitor Nephrotoxicity in Pediatric Kidney Transplant Recipients. Int J Mol Sci 2021; 22:ijms22115414. [PMID: 34063776 PMCID: PMC8196602 DOI: 10.3390/ijms22115414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 01/29/2023] Open
Abstract
Calcineurin inhibitors are highly efficacious immunosuppressive agents used in pediatric kidney transplantation. However, calcineurin inhibitor nephrotoxicity (CNIT) has been associated with the development of chronic renal allograft dysfunction and decreased graft survival. This study evaluated 37 formalin-fixed paraffin-embedded biopsies from pediatric kidney transplant recipients using gene expression profiling. Normal allograft samples (n = 12) served as negative controls and were compared to biopsies exhibiting CNIT (n = 11). The remaining samples served as positive controls to validate CNIT marker specificity and were characterized by other common causes of graft failure such as acute rejection (n = 7) and interstitial fibrosis/tubular atrophy (n = 7). MiRNA profiles served as the platform for data integration. Oxidative phosphorylation and mitochondrial dysfunction were the top molecular pathways associated with overexpressed genes in CNIT samples. Decreased ATP synthesis was identified as a significant biological function in CNIT, while key toxicology pathways included NRF2-mediated oxidative stress response and increased permeability transition of mitochondria. An integrative analysis demonstrated a panel of 13 significant miRNAs and their 33 CNIT-specific gene targets involved with mitochondrial activity and function. We also identified a candidate panel of miRNAs/genes, which may serve as future molecular markers for CNIT diagnosis as well as potential therapeutic targets.
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Cox SN, Chiurlia S, Divella C, Rossini M, Serino G, Bonomini M, Sirolli V, Aiello FB, Zaza G, Squarzoni I, Gangemi C, Stangou M, Papagianni A, Haas M, Schena FP. Formalin-fixed paraffin-embedded renal biopsy tissues: an underexploited biospecimen resource for gene expression profiling in IgA nephropathy. Sci Rep 2020; 10:15164. [PMID: 32938960 PMCID: PMC7494931 DOI: 10.1038/s41598-020-72026-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 01/01/2023] Open
Abstract
Primary IgA nephropathy (IgAN) diagnosis is based on IgA-dominant glomerular deposits and histological scoring is done on formalin-fixed paraffin embedded tissue (FFPE) sections using the Oxford classification. Our aim was to use this underexploited resource to extract RNA and identify genes that characterize active (endocapillary–extracapillary proliferations) and chronic (tubulo-interstitial) renal lesions in total renal cortex. RNA was extracted from archival FFPE renal biopsies of 52 IgAN patients, 22 non-IgAN and normal renal tissue of 7 kidney living donors (KLD) as controls. Genome-wide gene expression profiles were obtained and biomarker identification was carried out comparing gene expression signatures a subset of IgAN patients with active (N = 8), and chronic (N = 12) renal lesions versus non-IgAN and KLD. Bioinformatic analysis identified transcripts for active (DEFA4,TNFAIP6,FAR2) and chronic (LTB,CXCL6, ITGAX) renal lesions that were validated by RT-PCR and IHC. Finally, two of them (TNFAIP6 for active and CXCL6 for chronic) were confirmed in the urine of an independent cohort of IgAN patients compared with non-IgAN patients and controls. We have integrated transcriptomics with histomorphological scores, identified specific gene expression changes using the invaluable repository of archival renal biopsies and discovered two urinary biomarkers that may be used for specific clinical decision making.
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Affiliation(s)
- Sharon Natasha Cox
- Schena Foundation, Research Center of Kidney Diseases, Strada Provinciale Valenzano-Casamassima Km. 3.00, 70100, Valenzano, Bari, Italy. .,Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy.
| | - Samantha Chiurlia
- Schena Foundation, Research Center of Kidney Diseases, Strada Provinciale Valenzano-Casamassima Km. 3.00, 70100, Valenzano, Bari, Italy
| | - Chiara Divella
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Michele Rossini
- Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy
| | - Grazia Serino
- National Institute of Gastroenterology "S. de Bellis", Research Hospital, 70013, Castellana Grotte, Bari, Italy
| | - Mario Bonomini
- Department of Medicine and Aging Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Vittorio Sirolli
- Department of Medicine and Aging Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Francesca B Aiello
- Department of Medicine and Aging Sciences, University "G. D'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Gianluigi Zaza
- Renal Unit, Department of Medicine, University-Hospital of Verona, Verona, Italy
| | - Isabella Squarzoni
- Renal Unit, Department of Medicine, University-Hospital of Verona, Verona, Italy
| | - Concetta Gangemi
- Renal Unit, Department of Medicine, University-Hospital of Verona, Verona, Italy
| | - Maria Stangou
- Department of Nephrology, Hippokration General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Aikaterini Papagianni
- Department of Nephrology, Hippokration General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mark Haas
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Francesco Paolo Schena
- Schena Foundation, Research Center of Kidney Diseases, Strada Provinciale Valenzano-Casamassima Km. 3.00, 70100, Valenzano, Bari, Italy. .,Division of Nephrology, Dialysis, and Transplantation, Department of Emergency and Organ Transplantation, University of Bari, Bari, Italy.
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Challenges in Cancer Biomarker Discovery Exemplified by the Identification of Diagnostic MicroRNAs in Prostate Tissues. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9086829. [PMID: 32462034 PMCID: PMC7225851 DOI: 10.1155/2020/9086829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/20/2020] [Accepted: 04/25/2020] [Indexed: 12/23/2022]
Abstract
Identification and clinical translation of routinely tested biomarkers require a complex and multistep workflow. Here, we described a confirmatory process estimating the utility of previously identified candidate tissue miRNAs for diagnosis of prostate cancer (PCa). RNA was isolated from formalin-fixed paraffin-embedded (FFPE) prostate tissue surgically resected from 44 patients with PCa and 24 patients with benign prostate hyperplasia (BPH). Of the 92 RNA samples obtained, 68 represented 42 malignant (PCa) areas and 26 represented nonmalignant (PCa 0%) areas of the prostate tissue sections. The levels of miR-32-5p, miR-183-5p, miR-141-5p, miR-187-3p, miR-375, miR-663b, miR-615-3p, miR-205-5p, miR-221-3p, and miR-222-3p were evaluated using Exiqon chemistry. Five (miR-32-5p, miR-141-5p, miR-187-3p, miR-375, and miR-615-3p), one (miR-32-5p), and two (miR-32-5p and miR-141-5p) miRNAs discriminated between BPH and areas of cancer-bearing prostate tissue harboring different numbers of cancer cells (PCa 15–70%, PCa 2–10%, and PCA 0%, respectively), with an area under the receiver operating characteristics curve (AUC-ROC) > 0.9. Only miRNA 32-5p discriminated BPH specimens from sections of cancer-bearing prostate tissue with a low percentage, a high percentage, or no dysplastic cells. miR-32-5p could be considered as potential diagnostic biomarker discriminating BPH from noncancerous areas within cancer-bearing prostate tissue. However, further clinical studies are warranted to confirm its diagnostic utility.
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Identification of a Gene-Related Risk Signature in Melanoma Patients Using Bioinformatic Profiling. JOURNAL OF ONCOLOGY 2020; 2020:7526204. [PMID: 32411243 PMCID: PMC7206882 DOI: 10.1155/2020/7526204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/21/2020] [Indexed: 01/15/2023]
Abstract
Introduction Gene signature has been used to predict prognosis in melanoma patients. Meanwhile, the efficacy of immunotherapy was correlated with particular genes expression or mutation. In this study, we systematically explored the gene expression pattern in the melanoma-immune microenvironment and its relationship with prognosis. Methods A cohort of 122 melanoma cases with whole-genome microarray expression data were enrolled from the Gene Expression Omnibus (GEO) database. The findings were validated using The Cancer Genome Atlas (TCGA) database. A principal component analysis (PCA), gene set enrichment analysis (GSEA), and gene oncology (GO) analysis were performed to explore the bioinformatic implications. Results Different gene expression patterns were identified according to the clinical stage. All eligible gene sets were analyzed, and the 8 genes (GPR87, KIT, SH3GL3, PVRL1, ATP1B1, CDAN1, FAU, and TNFSF14) with the greatest prognostic impact on melanoma. A gene-related risk signature was developed to distinguish patients with a high or low risk of an unfavorable outcome, and this signature was validated using the TCGA database. Furthermore, the prognostic significance of the signature between the classified subgroups was verified as an independent prognostic predictor of melanoma. Additionally, the low-risk melanoma patients presented an enhanced immune phenotype compared to that of the high-risk gene signature patients. Conclusions The gene pattern differences in melanoma were profiled, and a gene signature that could independently predict melanoma patients with a high risk of poor survival was established, highlighting the relationship between prognosis and the local immune response.
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Jia G, Wang X, Li Q, Lu W, Tang X, Wistuba I, Xie Y. RCRnorm: An integrated system of random-coefficient hierarchical regression models for normalizing NanoString nCounter data. Ann Appl Stat 2019; 13:1617-1647. [PMID: 33564347 PMCID: PMC7869841 DOI: 10.1214/19-aoas1249] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) samples have great potential for biomarker discovery, retrospective studies, and diagnosis or prognosis of diseases. Their application, however, is hindered by the unsatisfactory performance of traditional gene expression profiling techniques on damaged RNAs. NanoString nCounter platform is well suited for profiling of FFPE samples and measures gene expression with high sensitivity, which may greatly facilitate realization of scientific and clinical values of FFPE samples. However, methodological development for normalization, a critical step when analyzing this type of data, is far behind. Existing methods designed for the platform use information from different types of internal controls separately and rely on an overly-simplified assumption that expression of housekeeping genes is constant across samples for global scaling. Thus, these methods are not optimized for the nCounter system, not mentioning that they were not developed for FFPE samples. We construct an integrated system of random-coefficient hierarchical regression models to capture main patterns and characteristics observed from NanoString data of FFPE samples, and develop a Bayesian approach to estimate parameters and normalize gene expression across samples. Our method, labeled RCRnorm, incorporates information from all aspects of the experimental design and simultaneously removes biases from various sources. It eliminates the unrealistic assumption on housekeeping genes and offers great interpretability. Furthermore, it is applicable to freshly frozen or like samples that can be generally viewed as a reduced case of FFPE samples. Simulation and applications showed the superior performance of RCRnorm.
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Affiliation(s)
- Gaoxiang Jia
- Department of Statistical Science, Southern Methodist University, 3225 Daniel Avenue, P O Box 750332, Dallas, Texas 75275
- Quantitative Biomedical Research Center, Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Xinlei Wang
- Department of Statistical Science, Southern Methodist University, 3225 Daniel Avenue, P O Box 750332, Dallas, Texas 75275
| | - Qiwei Li
- Quantitative Biomedical Research Center, Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Wei Lu
- Department of Translational Molecular Pathology, University of Texas, MD Anderson Cancer Center, Houston, Texas 77030
| | - Ximing Tang
- Department of Translational Molecular Pathology, University of Texas, MD Anderson Cancer Center, Houston, Texas 77030
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, University of Texas, MD Anderson Cancer Center, Houston, Texas 77030
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Chen R, Guan Q, Cheng J, He J, Liu H, Cai H, Hong G, Zhang J, Li N, Ao L, Guo Z. Robust transcriptional tumor signatures applicable to both formalin-fixed paraffin-embedded and fresh-frozen samples. Oncotarget 2018; 8:6652-6662. [PMID: 28036264 PMCID: PMC5351660 DOI: 10.18632/oncotarget.14257] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/02/2016] [Indexed: 12/19/2022] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable resource for clinical researches. However, FFPE samples are usually considered an unreliable source for gene expression analysis due to the partial RNA degradation. In this study, through comparing gene expression profiles between FFPE samples and paired fresh-frozen (FF) samples for three cancer types, we firstly showed that expression measurements of thousands of genes had at least two-fold change in FFPE samples compared with paired FF samples. Therefore, for a transcriptional signature based on risk scores summarized from the expression levels of the signature genes, the risk score thresholds trained from FFPE (or FF) samples could not be applied to FF (or FFPE) samples. On the other hand, we found that more than 90% of the relative expression orderings (REOs) of gene pairs in the FF samples were maintained in their paired FFPE samples and largely unaffected by the storage time. The result suggested that the REOs of gene pairs were highly robust against partial RNA degradation in FFPE samples. Finally, as a case study, we developed a REOs-based signature to distinguish liver cirrhosis from hepatocellular carcinoma (HCC) using FFPE samples. The signature was validated in four datasets of FFPE samples and eight datasets of FF samples. In conclusion, the valuable FFPE samples can be fully exploited to identify REOs-based diagnostic and prognostic signatures which could be robustly applicable to both FF samples and FFPE samples with degraded RNA.
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Affiliation(s)
- Rou Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Qingzhou Guan
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Jun Cheng
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Jun He
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Huaping Liu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Hao Cai
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Guini Hong
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Jiahui Zhang
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Na Li
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Lu Ao
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Zheng Guo
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
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Lawler K, Papouli E, Naceur-Lombardelli C, Mera A, Ougham K, Tutt A, Kimbung S, Hedenfalk I, Zhan J, Zhang H, Buus R, Dowsett M, Ng T, Pinder SE, Parker P, Holmberg L, Gillett CE, Grigoriadis A, Purushotham A. Gene expression modules in primary breast cancers as risk factors for organotropic patterns of first metastatic spread: a case control study. Breast Cancer Res 2017; 19:113. [PMID: 29029636 PMCID: PMC5640935 DOI: 10.1186/s13058-017-0881-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 07/12/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Metastases from primary breast cancers can involve single or multiple organs at metastatic disease diagnosis. Molecular risk factors for particular patterns of metastastic spread in a clinical population are limited. METHODS A case-control design including 1357 primary breast cancers was used to study three distinct clinical patterns of metastasis, which occur within the first six months of metastatic disease: bone and visceral metasynchronous spread, bone-only, and visceral-only metastasis. Whole-genome expression profiles were obtained using whole genome (WG)-DASL assays from formalin-fixed paraffin-embedded (FFPE) samples. A systematic protocol was developed for handling FFPE samples together with stringent data quality controls to identify robust expression profiling data. A panel of published and novel gene sets were tested for association with these specific patterns of metastatic spread and odds ratios (ORs) were calculated. RESULTS Metasynchronous metastasis to bone and viscera was found in all intrinsic breast cancer subtypes, while immunohistochemically (IHC)-defined receptor status and specific IntClust subgroups were risk factors for visceral-only or bone-only first metastases. Among gene modules, those related to proliferation increased the risk of metasynchronous metastasis (OR (95% CI) = 2.3 (1.1-4.8)) and visceral-only first metastasis (OR (95% CI) = 2.5 (1.2-5.1)) but not bone-only metastasis (OR (95% CI) = 0.97 (0.56-1.7)). A 21-gene module (BV) was identified in estrogen-receptor-positive breast cancers with metasynchronous metastasis to bone and viscera (area under the curve = 0.77), and its expression increased the risk of bone and visceral metasynchronous spread in this population. BV was further orthogonally validated with NanoString nCounter in primary breast cancers, and was reproducible in their matched lymph nodes metastases and an external cohort. CONCLUSION This case-control study of WG-DASL global expression profiles from FFPE tumour samples, after careful quality control and RNA selection, revealed that gene modules in the primary tumour have differing risks for clinical patterns of metasynchronous first metastases. Moreover, a novel gene module was identified as a putative risk factor for metasynchronous bone and visceral first metastatic spread, with potential implications for disease monitoring and treatment planning.
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Affiliation(s)
- Katherine Lawler
- School of Cancer Studies, CRUK King’s Health Partners Centre, King’s College London, Guy’s Campus, London, SE1 1UL UK
- Institute for Mathematical and Molecular Biomedicine, King’s College London, Hodgkin Building, Guy’s Campus, London, SE1 1UL UK
| | - Efterpi Papouli
- NIHR Comprehensive Biomedical Research Centre at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London, London, WC2R 2LS UK
| | - Cristina Naceur-Lombardelli
- Research Oncology, King’s College London, Faculty of Life Sciences and Medicine, Guy’s Hospital, London, SE1 9RT UK
| | - Anca Mera
- Research Oncology, King’s College London, Faculty of Life Sciences and Medicine, Guy’s Hospital, London, SE1 9RT UK
- Cancer Epidemiology Unit, King’s College London, Guy’s Hospital, Great Maze Pond, London, SE1 9RT UK
| | - Kayleigh Ougham
- Cancer Bioinformatics, King’s College London, Innovation Centre, Cancer Centre at Guy’s Hospital, London, SE1 9RT UK
| | - Andrew Tutt
- Breast Cancer Now Research Unit, Innovation Centre, Cancer Centre at Guy’s Hospital, King’s Health Partners AHSC, King’s College London, Faculty of Life Sciences and Medicine, London, SE1 9RT UK
| | - Siker Kimbung
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden
| | - Jun Zhan
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education of Beijing, Beijing, People’s Republic of China, Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Hongquan Zhang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education of Beijing, Beijing, People’s Republic of China, Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, Peking University Health Science Center, Beijing, People’s Republic of China
| | - Richard Buus
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Mitch Dowsett
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Tony Ng
- School of Cancer Studies, CRUK King’s Health Partners Centre, King’s College London, Guy’s Campus, London, SE1 1UL UK
- Breast Cancer Now Research Unit, Innovation Centre, Cancer Centre at Guy’s Hospital, King’s Health Partners AHSC, King’s College London, Faculty of Life Sciences and Medicine, London, SE1 9RT UK
- Richard Dimbleby Department of Cancer Research, Randall Division of Cell and Molecular Biophysics, King’s College London, Guy’s Campus, London, SE1 1UL UK
- UCL Cancer Institute, Paul O’Gorman Building, University College London, London, WC1E 6DD UK
| | - Sarah E. Pinder
- Research Oncology, King’s College London, Faculty of Life Sciences and Medicine, Guy’s Hospital, London, SE1 9RT UK
| | - Peter Parker
- School of Cancer Studies, CRUK King’s Health Partners Centre, King’s College London, Guy’s Campus, London, SE1 1UL UK
- London Research Institute, Lincoln’s Inn Fields, London, WC2A 3LY UK
| | - Lars Holmberg
- Cancer Epidemiology Unit, King’s College London, Guy’s Hospital, Great Maze Pond, London, SE1 9RT UK
- Uppsala University, Department of Surgical Sciences, Uppsala University Hospital, 751 85 Uppsala, Sweden
| | - Cheryl E. Gillett
- Research Oncology, King’s College London, Faculty of Life Sciences and Medicine, Guy’s Hospital, London, SE1 9RT UK
| | - Anita Grigoriadis
- School of Cancer Studies, CRUK King’s Health Partners Centre, King’s College London, Guy’s Campus, London, SE1 1UL UK
- Research Oncology, King’s College London, Faculty of Life Sciences and Medicine, Guy’s Hospital, London, SE1 9RT UK
- Cancer Bioinformatics, King’s College London, Innovation Centre, Cancer Centre at Guy’s Hospital, London, SE1 9RT UK
- Breast Cancer Now Research Unit, Innovation Centre, Cancer Centre at Guy’s Hospital, King’s Health Partners AHSC, King’s College London, Faculty of Life Sciences and Medicine, London, SE1 9RT UK
| | - Arnie Purushotham
- School of Cancer Studies, CRUK King’s Health Partners Centre, King’s College London, Guy’s Campus, London, SE1 1UL UK
- Research Oncology, King’s College London, Faculty of Life Sciences and Medicine, Guy’s Hospital, London, SE1 9RT UK
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11
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Lin-Wang HT, Cipullo R, Dinkhuysen JJ, Finger MA, Rossi JM, Correia EB, Hirata MH. Down regulation of protective genes is associated with cellular and antibody-mediated rejection. Clin Transplant 2017; 31. [DOI: 10.1111/ctr.13060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Hui Tzu Lin-Wang
- Laboratory of Molecular Investigation in Cardiology; Dante Pazzanese Institute of Cardiology; São Paulo Brazil
| | - Reginaldo Cipullo
- Department of Heart Transplantation; Dante Pazzanese Institute of Cardiology; São Paulo Brazil
| | - Jarbas J. Dinkhuysen
- Department of Heart Transplantation; Dante Pazzanese Institute of Cardiology; São Paulo Brazil
| | - Marco A. Finger
- Department of Heart Transplantation; Dante Pazzanese Institute of Cardiology; São Paulo Brazil
| | - João M. Rossi
- Department of Heart Transplantation; Dante Pazzanese Institute of Cardiology; São Paulo Brazil
| | - Edileide B. Correia
- Department of Heart Transplantation; Dante Pazzanese Institute of Cardiology; São Paulo Brazil
| | - Mário H. Hirata
- Laboratory of Molecular Investigation in Cardiology; Dante Pazzanese Institute of Cardiology; São Paulo Brazil
- School of Pharmaceutical Sciences; University of São Paulo; São Paulo Brazil
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12
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Laginestra MA, Tripodo C, Agostinelli C, Motta G, Hartmann S, Döring C, Rossi M, Melle F, Sapienza MR, Tabanelli V, Pileri A, Fuligni F, Gazzola A, Mannu C, Sagramoso CA, Lonardi S, Lorenzi L, Bacci F, Sabattini E, Borges A, Simonitsch-Klupp I, Cabecadas J, Campo E, Rosai J, Hansmann ML, Facchetti F, Pileri SA. Distinctive Histogenesis and Immunological Microenvironment Based on Transcriptional Profiles of Follicular Dendritic Cell Sarcomas. Mol Cancer Res 2017; 15:541-552. [DOI: 10.1158/1541-7786.mcr-16-0301] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 12/02/2016] [Accepted: 12/15/2016] [Indexed: 11/16/2022]
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13
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Riva N, Clarelli F, Domi T, Cerri F, Gallia F, Trimarco A, Brambilla P, Lunetta C, Lazzerini A, Lauria G, Taveggia C, Iannaccone S, Nobile-Orazio E, Comi G, D’Antonio M, Martinelli-Boneschi F, Quattrini A. Unraveling gene expression profiles in peripheral motor nerve from amyotrophic lateral sclerosis patients: insights into pathogenesis. Sci Rep 2016; 6:39297. [PMID: 27982123 PMCID: PMC5159906 DOI: 10.1038/srep39297] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 11/21/2016] [Indexed: 01/12/2023] Open
Abstract
The aim of the present study is to investigate the molecular pathways underlying amyotrophic lateral sclerosis (ALS) pathogenesis within the peripheral nervous system. We analyzed gene expression changes in human motor nerve diagnostic biopsies obtained from eight ALS patients and seven patients affected by motor neuropathy as controls. An integrated transcriptomics and system biology approach was employed. We identified alterations in the expression of 815 genes, with 529 up-regulated and 286 down-regulated in ALS patients. Up-regulated genes clustered around biological process involving RNA processing and protein metabolisms. We observed a significant enrichment of up-regulated small nucleolar RNA transcripts (p = 2.68*10-11) and genes related to endoplasmic reticulum unfolded protein response and chaperone activity. We found a significant down-regulation in ALS of genes related to the glutamate metabolism. Interestingly, a network analysis highlighted HDAC2, belonging to the histone deacetylase family, as the most interacting node. While so far gene expression studies in human ALS have been performed in postmortem tissues, here specimens were obtained from biopsy at an early phase of the disease, making these results new in the field of ALS research and therefore appealing for gene discovery studies.
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Affiliation(s)
- Nilo Riva
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Ferdinando Clarelli
- Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Teuta Domi
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Federica Cerri
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Gallia
- 2Neurology, IRCCS Istituto Clinico Humanitas, Milano University, Milan, Italy
| | - Amelia Trimarco
- Axo-glia interactions Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Paola Brambilla
- Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Christian Lunetta
- NEuroMuscular Omnicentre (NEMO), Niguarda Ca Granda Hospital, Milan, Italy
| | - Alberto Lazzerini
- Hand Surgery and Microsurgery Unit, IRCCS Humanitas Clinical Institute, Milan, Italy
| | - Giuseppe Lauria
- 3rd Neurology Unit, IRCCS Foundation “Carlo Besta” Neurological Institute, Milan, Italy
| | - Carla Taveggia
- Axo-glia interactions Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Sandro Iannaccone
- Department of Clinical Neurosciences, San Raffaele Scientific Institute, Milan, Italy
| | | | - Giancarlo Comi
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
- Universita` Vita e Salute San Raffaele, Milan, Italy
| | - Maurizio D’Antonio
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Filippo Martinelli-Boneschi
- Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Angelo Quattrini
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
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14
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Piccaluga PP, Navari M, De Falco G, Ambrosio MR, Lazzi S, Fuligni F, Bellan C, Rossi M, Sapienza MR, Laginestra MA, Etebari M, Rogena EA, Tumwine L, Tripodo C, Gibellini D, Consiglio J, Croce CM, Pileri SA, Leoncini L. Virus-encoded microRNA contributes to the molecular profile of EBV-positive Burkitt lymphomas. Oncotarget 2016; 7:224-40. [PMID: 26325594 PMCID: PMC4807994 DOI: 10.18632/oncotarget.4399] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/20/2015] [Indexed: 01/28/2023] Open
Abstract
Burkitt lymphoma (BL) is an aggressive neoplasm characterized by consistent morphology and phenotype, typical clinical behavior and distinctive molecular profile. The latter is mostly driven by the MYC over-expression associated with the characteristic translocation (8;14) (q24; q32) or with variant lesions. Additional genetic events can contribute to Burkitt Lymphoma pathobiology and retain clinical significance. A pathogenetic role for Epstein-Barr virus infection in Burkitt lymphomagenesis has been suggested; however, the exact function of the virus is largely unknown. In this study, we investigated the molecular profiles (genes and microRNAs) of Epstein-Barr virus-positive and -negative BL, to identify specific patterns relying on the differential expression and role of Epstein-Barr virus-encoded microRNAs. First, we found significant differences in the expression of viral microRNAs and in selected target genes. Among others, we identified LIN28B, CGNL1, GCET2, MRAS, PLCD4, SEL1L, SXX1, and the tyrosine kinases encoding STK10/STK33, all provided with potential pathogenetic significance. GCET2, also validated by immunohistochemistry, appeared to be a useful marker for distinguishing EBV-positive and EBV-negative cases. Further, we provided solid evidences that the EBV-encoded microRNAs (e.g. BART6) significantly mold the transcriptional landscape of Burkitt Lymphoma clones. In conclusion, our data indicated significant differences in the transcriptional profiles of EBV-positive and EBV-negative BL and highlight the role of virus encoded miRNA.
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Affiliation(s)
- Pier Paolo Piccaluga
- Hematopathology Section, Department of Experimental, Diagnostic, and Experimental Medicine, S. Orsola-Malpighi Hospital, Bologna University School of Medicine, Bologna, Italy
| | - Mohsen Navari
- Hematopathology Section, Department of Experimental, Diagnostic, and Experimental Medicine, S. Orsola-Malpighi Hospital, Bologna University School of Medicine, Bologna, Italy.,Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Giulia De Falco
- Department of Medical Biotechnology, University of Siena, Siena, Italy.,School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | | | - Stefano Lazzi
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Fabio Fuligni
- Hematopathology Section, Department of Experimental, Diagnostic, and Experimental Medicine, S. Orsola-Malpighi Hospital, Bologna University School of Medicine, Bologna, Italy
| | - Cristiana Bellan
- Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Maura Rossi
- Hematopathology Section, Department of Experimental, Diagnostic, and Experimental Medicine, S. Orsola-Malpighi Hospital, Bologna University School of Medicine, Bologna, Italy
| | - Maria Rosaria Sapienza
- Hematopathology Section, Department of Experimental, Diagnostic, and Experimental Medicine, S. Orsola-Malpighi Hospital, Bologna University School of Medicine, Bologna, Italy
| | - Maria Antonella Laginestra
- Hematopathology Section, Department of Experimental, Diagnostic, and Experimental Medicine, S. Orsola-Malpighi Hospital, Bologna University School of Medicine, Bologna, Italy
| | - Maryam Etebari
- Hematopathology Section, Department of Experimental, Diagnostic, and Experimental Medicine, S. Orsola-Malpighi Hospital, Bologna University School of Medicine, Bologna, Italy
| | - Emily A Rogena
- Department of Pathology, University of Nairobi, Nairobi, Kenya
| | | | - Claudio Tripodo
- Tumour Immunology Unit, Department of Health Science, Human Pathology Section, Palermo University School of Medicine, Palermo, Italy
| | - Davide Gibellini
- Department of Pathology and Diagnostic, University of Verona, Verona, Italy
| | - Jessica Consiglio
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Carlo M Croce
- Department of Molecular Virology, Immunology, and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Stefano A Pileri
- Diagnostic Hematopathology Unit, European Institute of Oncology, Milan, Italy
| | - Lorenzo Leoncini
- Department of Medical Biotechnology, University of Siena, Siena, Italy
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15
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Rubicz R, Zhao S, Wright JL, Coleman I, Grasso C, Geybels MS, Leonardson A, Kolb S, April C, Bibikova M, Troyer D, Lance R, Lin DW, Ostrander EA, Nelson PS, Fan JB, Feng Z, Stanford JL. Gene expression panel predicts metastatic-lethal prostate cancer outcomes in men diagnosed with clinically localized prostate cancer. Mol Oncol 2016; 11:140-150. [PMID: 28145099 PMCID: PMC5510189 DOI: 10.1002/1878-0261.12014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 08/30/2016] [Indexed: 11/24/2022] Open
Abstract
Prognostic biomarkers are needed to distinguish patients with clinically localized prostate cancer (PCa) who are at high risk of metastatic progression. The tumor transcriptome may reveal its aggressiveness potential and have utility for predicting adverse patient outcomes. Genomewide gene expression levels were measured in primary tumor samples of 383 patients in a population‐based discovery cohort, and from an independent clinical validation dataset of 78 patients. Patients were followed for ≥ 5 years after radical prostatectomy to ascertain outcomes. Area under the receiver‐operating characteristic curve (AUC), partial AUC (pAUC, 95% specificity), and P‐value criteria were used to detect and validate the differentially expressed transcripts. Twenty‐three differentially expressed transcripts in patients with metastatic‐lethal compared with nonrecurrent PCa were validated (P < 0.05; false discovery rate < 0.20) in the independent dataset. The addition of each validated transcript to a model with Gleason score showed that 17 transcripts significantly improved the AUC (range: 0.83–0.88; all P‐values < 0.05). These differentially expressed mRNAs represent genes with diverse cellular functions related to tumor aggressiveness. This study validated 23 gene transcripts for predicting metastatic‐lethal PCa in patients surgically treated for clinically localized disease. Several of these mRNA biomarkers have clinical potential for identifying the subset of PCa patients with more aggressive tumors who would benefit from closer monitoring and adjuvant therapy.
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Affiliation(s)
- Rohina Rubicz
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Shanshan Zhao
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA
| | - Jonathan L Wright
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Urology, University of Washington School of Medicine, Seattle, WA, USA
| | - Ilsa Coleman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Catherine Grasso
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Milan S Geybels
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Epidemiology, GROW School for Oncology and Developmental Biology, Maastricht University, The Netherlands
| | - Amy Leonardson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | - Dean Troyer
- Departments of Pathology and Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Raymond Lance
- Department of Urology, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Daniel W Lin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Urology, University of Washington School of Medicine, Seattle, WA, USA
| | - Elaine A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Ziding Feng
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
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16
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Shahabi A, Lewinger JP, Ren J, April C, Sherrod AE, Hacia JG, Daneshmand S, Gill I, Pinski JK, Fan JB, Stern MC. Novel Gene Expression Signature Predictive of Clinical Recurrence After Radical Prostatectomy in Early Stage Prostate Cancer Patients. Prostate 2016; 76:1239-56. [PMID: 27272349 PMCID: PMC9015679 DOI: 10.1002/pros.23211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/16/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND Current clinical tools have limited accuracy in differentiating patients with localized prostate cancer who are at risk of recurrence from patients with indolent disease. We aimed to identify a gene expression signature that jointly with clinical variables could improve upon the prediction of clinical recurrence after RP for patients with stage T2 PCa. METHODS The study population includes consented patients who underwent a radical retropubic prostatectomy (RP) and bilateral pelvic lymph node dissection at the University of Southern California in the PSA-era (1988-2008). We used a nested case-control study of 187 organ-confined patients (pT2N0M0): 154 with no recurrence ("controls") and 33 with clinical recurrence ("cases"). RNA was obtained from laser capture microdissected malignant glands representative of the overall Gleason score of each patient. Whole genome gene expression profiles (29,000 transcripts) were obtained using the Whole Genome DASL HT platform (Illumina, Inc). A gene expression signature of PCa clinical recurrence was identified using stability selection with elastic net regularized logistic regression. Three existing datasets generated with the Affymetrix Human Exon 1.0ST array were used for validation: Mayo Clinic (MC, n = 545), Memorial Sloan Kettering Cancer Center (SKCC, n = 150), and Erasmus Medical Center (EMC, n = 48). The areas under the ROC curve (AUCs) were obtained using repeated fivefold cross-validation. RESULTS A 28-gene expression signature was identified that jointly with key clinical variables (age, Gleason score, pre-operative PSA level, and operation year) was predictive of clinical recurrence (AUC of clinical variables only was 0.67, AUC of clinical variables, and 28-gene signature was 0.99). The AUC of this gene signature fitted in each of the external datasets jointly with clinical variables was 0.75 (0.72-0.77) (MC), 0.90 (0.86-0.94) (MSKCC), and 0.82 (0.74-0.91) (EMC), whereas the AUC for clinical variables only in each dataset was 0.72 (0.70-0.74), 0.86 (0.82-0.91), and 0.76 (0.67-0.85), respectively. CONCLUSIONS We report a novel gene-expression based classifier identified using agnostic approaches from whole genome expression profiles that can improve upon the accuracy of clinical indicators to stratify early stage localized patients at risk of clinical recurrence after RP. Prostate 76:1239-1256, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ahva Shahabi
- Department of Preventive Medicine, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, Los Angeles, California
| | - Juan Pablo Lewinger
- Department of Preventive Medicine, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, Los Angeles, California
| | - Jie Ren
- Department of Preventive Medicine, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, Los Angeles, California
| | | | - Andy E. Sherrod
- Department of Pathology, Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, California
| | - Joseph G. Hacia
- Department of Biochemistry and Molecular Biology, Keck School of Medicine of USC, Los Angeles, California
| | - Siamak Daneshmand
- Department of Urology and USC Institute of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, California
| | - Inderbir Gill
- Department of Urology and USC Institute of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, California
| | - Jacek K. Pinski
- Department of Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, California
| | - Jian-Bing Fan
- Illumina, Inc., San Diego, California
- AnchorDx Corporation, Guangzhou, China
| | - Mariana C. Stern
- Department of Preventive Medicine, Keck School of Medicine of USC, Norris Comprehensive Cancer Center, Los Angeles, California
- Department of Urology and USC Institute of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Los Angeles, California
- Correspondence to: Dr. Mariana C. Stern, University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, 1441 Eastlake Avenue, Room 5421A, Los Angeles, CA 90089.
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17
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Iddawela M, Rueda OM, Klarqvist M, Graf S, Earl HM, Caldas C. Reliable gene expression profiling of formalin-fixed paraffin-embedded breast cancer tissue (FFPE) using cDNA-mediated annealing, extension, selection, and ligation whole-genome (DASL WG) assay. BMC Med Genomics 2016; 9:54. [PMID: 27542606 PMCID: PMC4992321 DOI: 10.1186/s12920-016-0215-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/05/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The difficulties in using formalin-fixed and paraffin-embedded (FFPE) tumour specimens for molecular marker studies have hampered progress in translational cancer research. The cDNA-mediated, annealing, selection, extension, and ligation (DASL) assay is a platform for gene expression profiling from FFPE tissue and hence could allow analysis of large collections of tissue with associated clinical data from existing archives, therefore facilitating the development of novel biomarkers. METHOD RNA isolated from matched fresh frozen (FF) and FFPE cancer specimens was profiled using both the DASL whole-genome (WG) platform, and Illumina BeadArray's, and results were compared. Samples utilized were obtained from the breast cancer tumour bank held at the Cambridge University Hospitals NHS Foundation Trust. RESULTS The number of reliably detected probes was comparable between the DASL and BeadArray platforms, indicating that the source of RNA did not result in a significant difference in the detection rates (Mean probes- 17114 in FFPE & 17400 in FF). There was a significant degree of correlation between replicates within the FF and FFPE sample sets (r (2) = 0.96-0.98) as well as between the two platforms (DASL vs. BeadArray r (2) = range 0.83-0.89). Hierarchical clustering using the most informative probes showed that replicate and matched samples were grouped into the same sub-cluster, regardless of whether RNA was derived from FF or FFPE tissue. CONCLUSION Both FF and FFPE material generated reproducible gene expression profiles, although there was more noise in profiles from FFPE specimens. We have shown that the DASL WG platform is suitable for profiling formalin-fixed paraffin-embedded samples, but robust bioinformatics analysis is required.
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Affiliation(s)
- Mahesh Iddawela
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
- Department of Oncology, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge, CB1 9RN UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800 Australia
- School of Clinical Sciences, Monash University, Clayton, Victoria Australia
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Marcus Klarqvist
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Stefan Graf
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
| | - Helena M. Earl
- Department of Oncology, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge, CB1 9RN UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE UK
- Department of Oncology, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge, CB1 9RN UK
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge, UK
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18
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Curci C, Sallustio F, Serino G, De Palma G, Trpevski M, Fiorentino M, Rossini M, Quaglia M, Valente M, Furian L, Toscano A, Mazzucco G, Barreca A, Bussolino S, Gesualdo L, Stratta P, Rigotti P, Citterio F, Biancone L, Schena FP. Potential role of effector memory T cells in chronic T cell-mediated kidney graft rejection. Nephrol Dial Transplant 2016; 31:2131-2142. [DOI: 10.1093/ndt/gfw245] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/12/2016] [Indexed: 11/14/2022] Open
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Pop LA, Pileczki V, Cojocneanu-Petric RM, Petrut B, Braicu C, Jurj AM, Buiga R, Achimas-Cadariu P, Berindan-Neagoe I. Normalization of gene expression measurement of tissue samples obtained by transurethral resection of bladder tumors. Onco Targets Ther 2016; 9:3369-80. [PMID: 27330317 PMCID: PMC4898429 DOI: 10.2147/ott.s97519] [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: 01/20/2023] Open
Abstract
Background Sample processing is a crucial step for all types of genomic studies. A major challenge for researchers is to understand and predict how RNA quality affects the identification of transcriptional differences (by introducing either false-positive or false-negative errors). Nanotechnologies help improve the quality and quantity control for gene expression studies. Patients and methods The study was performed on 14 tumor and matched normal pairs of tissue from patients with bladder urothelial carcinomas. We assessed the RNA quantity by using the NanoDrop spectrophotometer and the quality by nano-microfluidic capillary electrophoresis technology provided by Agilent 2100 Bioanalyzer. We evaluated the amplification status of three housekeeping genes and one small nuclear RNA gene using the ViiA 7 platform, with specific primers. Results Every step of the sample handling protocol, which begins with sample harvest and ends with the data analysis, is of utmost importance due to the fact that it is time consuming, labor intensive, and highly expensive. High temperature of the surgical procedure does not affect the small nucleic acid sequences in comparison with the mRNA. Conclusion Gene expression is clearly affected by the RNA quality, but less affected in the case of small nuclear RNAs. We proved that the high-temperature, highly invasive transurethral resection of bladder tumor procedure damages the tissue and affects the integrity of the RNA from biological specimens.
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Affiliation(s)
- Laura A Pop
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Valentina Pileczki
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania; Department of Analytical Chemistry, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Roxana M Cojocneanu-Petric
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Bogdan Petrut
- Department of Surgery II - Urology, The Oncology Institute "Prof Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania; Department of Urology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Cornelia Braicu
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Ancuta M Jurj
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Rares Buiga
- Department of Pathology, The Oncology Institute "Prof. Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania
| | - Patriciu Achimas-Cadariu
- Department of Surgery, The Oncology Institute "Prof Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania; Department of Surgical Oncology and Gynecological Oncology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Ioana Berindan-Neagoe
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania; Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania
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20
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A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay. Int J Mol Sci 2016; 17:ijms17050724. [PMID: 27187374 PMCID: PMC4881546 DOI: 10.3390/ijms17050724] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/02/2016] [Accepted: 05/04/2016] [Indexed: 12/24/2022] Open
Abstract
Mammary neoplasms are the tumors most affecting female dogs and women. Formalin-fixed, paraffin-embedded (FFPE) tissues are an invaluable source of archived biological material. Fresh frozen (FF) tissue is considered ideal for gene expression analysis. However, strategies based on FFPE material offer several advantages. Branched-DNA assays permit a reliable and fast workflow when analyzing gene expression. The aim of this study was to assess the comparability of the branched-DNA assay when analyzing certain gene expression patterns between FF and FFPE samples in canine mammary tumors. RNA was isolated from 109 FFPE samples and from 93 FF samples of different canine mammary tissues. Sixteen (16) target genes (Tp53; Myc; HMGA1; Pik3ca; Mcl1; MAPK3; FOXO3; PTEN; GATA4; PFDN5; HMGB1; MAPK1; BRCA2; BRCA1; HMGA2; and Her2) were analyzed via branched-DNA assay (b-DNA). ACTB, GAPDH, and HPRT1 were used as data normalizers. Overall, the relative gene expression of the two different origins of samples showed an agreement of 63%. Still, care should be taken, as FFPE specimens showed lower expression of the analyzed targets when compared to FF samples. The fact that the gene expression in FFPE proved to be lower than in FF specimens is likely to have been caused by the effect of storage time. ACTB had the best performance as a data normalizer.
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21
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Characterization of gene expression profiling of mouse tissues obtained during the postmortem interval. Exp Mol Pathol 2016; 100:482-92. [PMID: 27185020 DOI: 10.1016/j.yexmp.2016.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/13/2016] [Indexed: 12/27/2022]
Abstract
Attempts to establish a tissue bank from autopsy samples have led to uncovering of the secrets of many diseases. Here, we examined the length of time that the RNA from postmortem tissues is available for microarray analysis and reported the gene expression profile for up- and down-regulated genes during the postmortem interval. We extracted RNA from fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) brains and livers of three different groups of mice: 1) mice immediately after death, 2) mice that were stored at room temperature for 3h after death, and 3) mice that were stored at 4°C for 18h after death, as this storage resembles the human autopsy process in Japan. The RNA quality of the brain and the liver was maintained up to 18h during the postmortem interval. Based on the microarray analysis, we selected genes that were altered by >1.3-fold or <0.77-fold and classified these genes using hierarchical cluster analysis following DAVID gene ontology analysis. These studies revealed that cytoskeleton-related genes were enriched in the set of up-regulated genes, while serine protease inhibitors were enriched in the set of down-regulated genes. Interestingly, although the RNA quality was maintained due to high RNA integrity number (RIN) values, up-regulated genes were not validated by quantitative PCR, suggesting that these genes may become fragmented or modified by an unknown mechanism. Taken together, our findings suggest that under typical autopsy conditions, gene expression profiles that reflect disease pathology can be examined by understanding comprehensive recognition of postmortem fluctuation of gene expression.
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Mustafa DAM, Sieuwerts AM, Smid M, de Weerd V, van der Weiden M, Meijer - van Gelder ME, Martens JWM, Foekens JA, Kros JM. A Method to Correlate mRNA Expression Datasets Obtained from Fresh Frozen and Formalin-Fixed, Paraffin-Embedded Tissue Samples: A Matter of Thresholds. PLoS One 2015; 10:e0144097. [PMID: 26716838 PMCID: PMC4696787 DOI: 10.1371/journal.pone.0144097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/12/2015] [Indexed: 11/19/2022] Open
Abstract
Background Gene expression profiling of tumors is a successful tool for the discovery of new cancer biomarkers and potential targets for the development of new therapeutic strategies. Reliable profiling is preferably performed on fresh frozen (FF) tissues in which the quality of nucleic acids is better preserved than in formalin-fixed paraffin-embedded (FFPE) material. However, since snap-freezing of biopsy materials is often not part of daily routine in pathology laboratories, one may have to rely on archival FFPE material. Procedures to retrieve the RNAs from FFPE materials have been developed and therefore, datasets obtained from FFPE and FF materials need to be made compatible to ensure reliable comparisons are possible. Aim To develop an efficient method to compare gene expression profiles obtained from FFPE and FF samples using the same platform. Methods Twenty-six FFPE-FF sample pairs of the same tumors representing various cancer types, and two FFPE-FF sample pairs of breast cancer cell lines, were included. Total RNA was extracted and gene expression profiling was carried out using Illumina’s Whole-Genome cDNA-mediated Annealing, Selection, extension and Ligation (WG-DASL) V3 arrays, enabling the simultaneous detection of 24,526 mRNA transcripts. A sample exclusion criterion was created based on the expression of 11 stably expressed reference genes. Pearson correlation at the probe level was calculated for paired FFPE-FF, and three cut-off values were chosen. Spearman correlation coefficients between the matched FFPE and FF samples were calculated for three probe lists with varying levels of significance and compared to the correlation based on all measured probes. Unsupervised hierarchical cluster analysis was performed to verify performance of the included probe lists to compare matched FPPE-FF samples. Results Twenty-seven FFPE-FF pairs passed the sample exclusion criterion. From the profiles of 27 FFPE and FF matched samples, the best correlating probes were identified for various levels of significance (Pearson P<0.01, n = 1,432; P<0.05, n = 2,530; and P<0.10, n = 3,351 probes). Unsupervised hierarchical clustering of the 27 pairs using the resulting probes yielded 25, 21, and 19 correctly clustered pairs, respectively, compared to 1 pair when all probes were used. Conclusion The proposed method enables comparison of gene expression profiles of FFPE and/or FF origin measured on the same platform.
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Affiliation(s)
- Dana A. M. Mustafa
- Dept. of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- * E-mail:
| | - Anieta M. Sieuwerts
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel Smid
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Vania de Weerd
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | | | - John W. M. Martens
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John A. Foekens
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Johan M. Kros
- Dept. of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
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Goossens N, Nakagawa S, Hoshida Y. Molecular prognostic prediction in liver cirrhosis. World J Gastroenterol 2015; 21:10262-10273. [PMID: 26420954 PMCID: PMC4579874 DOI: 10.3748/wjg.v21.i36.10262] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Revised: 06/12/2015] [Accepted: 08/31/2015] [Indexed: 02/06/2023] Open
Abstract
The natural history of cirrhosis varies and therefore prognostic prediction is critical given the sizable patient population. A variety of clinical prognostic indicators have been developed and enable patient risk stratification although their performance is somewhat limited especially within relatively earlier stage of disease. Molecular prognostic indicators are expected to refine the prediction, and potentially link a subset of patients with molecular targeted interventions that counteract poor prognosis. Here we overview clinical and molecular prognostic indicators in the literature, and discuss critical issues to successfully define, evaluate, and deploy prognostic indicators as clinical scores or tests. The use of liver biopsy has been diminishing due to sampling variability on fibrosis assessment and emergence of imaging- or lab test-based fibrosis assessment methods. However, recent rapid developments of genomics technologies and selective molecular targeted agents has highlighted the need for biopsy tissue specimen to explore and establish molecular information-guided personalized/stratified clinical care, and eventually achieve “precision medicine”.
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24
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Rubicz R, Zhao S, April C, Wright JL, Kolb S, Coleman I, Lin DW, Nelson PS, Ostrander EA, Feng Z, Fan JB, Stanford JL. Expression of cell cycle-regulated genes and prostate cancer prognosis in a population-based cohort. Prostate 2015; 75:1354-62. [PMID: 25990700 PMCID: PMC4992473 DOI: 10.1002/pros.23016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 04/17/2015] [Indexed: 01/31/2023]
Abstract
BACKGROUND Prostate cancer (PCa) is clinically and biologically heterogeneous, making it difficult to predict at detection whether it will take an indolent or aggressive disease course. Cell cycle-regulated genes may be more highly expressed in actively dividing cells, with transcript levels reflecting tumor growth rate. Here, we evaluated expression of cell cycle genes in relation to PCa outcomes in a population-based cohort. METHODS Gene expression data were generated from tumor tissues obtained at radical prostatectomy for 383 population-based patients (12.3-years average follow-up). The overall mean and individual transcript levels of 30 selected cell cycle genes was compared between patients with no evidence of recurrence (73%) and those who recurred (27%) or died (7%) from PCa. RESULTS The multivariate adjusted hazard ratio (HR) for a change from the 25th to 75th percentile of mean gene expression level (range 8.02-10.05) was 1.25 (95%CI 0.96-1.63; P = 0.10) for PCa recurrence risk, and did not vary substantially by Gleason score, TMPRSS2-ERG fusion status, or family history of PCa. For lethal PCa, the HR for a change (25th to 75th percentile) in mean gene expression level was 2.04 (95%CI 1.26-3.31; P = 0.004), adjusted for clinicopathological variables. The ROC curve for mean gene expression level alone (AUC = 0.740) did not perform as well as clinicopathological variables alone (AUC = 0.803) for predicting lethal PCa, and the addition of mean gene expression to clinicopathological variables did not substantially improve prediction (AUC = 0.827; P = 0.18). Higher TK1 expression was strongly associated with both recurrent (P = 6.7 × 10(-5)) and lethal (P = 6.4 × 10(-6)) PCa. CONCLUSIONS Mean expression level for 30 selected cell cycle-regulated genes was unrelated to recurrence risk, but was associated with a twofold increase in risk of lethal PCa. However, gene expression had less discriminatory accuracy than clinical variables alone for predicting lethal events. Transcript levels for several genes in the panel were significantly overexpressed in lethal versus non-recurrent PCa.
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Affiliation(s)
- Rohina Rubicz
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Shanshan Zhao
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Jonathan L. Wright
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Urology, University of Washington School of Medicine, Seattle, WA
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Ilsa Coleman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Daniel W. Lin
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Urology, University of Washington School of Medicine, Seattle, WA
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Elaine A. Ostrander
- Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD
| | - Ziding Feng
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Janet L. Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA
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Abstract
With the emergence of genomic profiling technologies and selective molecular targeted therapies, biomarkers play an increasingly important role in the clinical management of cancer patients. Single gene/protein or multi-gene "signature"-based assays have been introduced to measure specific molecular pathway deregulations that guide therapeutic decision-making as predictive biomarkers. Genome-based prognostic biomarkers are also available for several cancer types for potential incorporation into clinical prognostic staging systems or practice guidelines. However, there is still a large gap between initial biomarker discovery studies and their clinical translation due to the challenges in the process of cancer biomarker development. In this review we summarize the steps of biomarker development, highlight key issues in successful validation and implementation, and overview representative examples in the oncology field. We also discuss regulatory issues and future perspectives in the era of big data analysis and precision medicine.
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Affiliation(s)
- Nicolas Goossens
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Division of Gastroenterology and Hepatology, Geneva University Hospital, Geneva, Switzerland
| | - Shigeki Nakagawa
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Xiaochen Sun
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Yujin Hoshida
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA
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26
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Vaca-Paniagua F, Alvarez-Gomez RM, Maldonado-Martínez HA, Pérez-Plasencia C, Fragoso-Ontiveros V, Lasa-Gonsebatt F, Herrera LA, Cantú D, Bargallo-Rocha E, Mohar A, Durand G, Forey N, Voegele C, Vallée M, Le Calvez-Kelm F, McKay J, Ardin M, Villar S, Zavadil J, Olivier M. Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues. PLoS One 2015; 10:e0126762. [PMID: 25961742 PMCID: PMC4427337 DOI: 10.1371/journal.pone.0126762] [Citation(s) in RCA: 13] [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: 01/12/2015] [Accepted: 04/07/2015] [Indexed: 12/27/2022] Open
Abstract
Triple negative breast cancer (TNBC), defined by the lack of expression of the estrogen receptor, progesterone receptor and human epidermal receptor 2, is an aggressive form of breast cancer that is more prevalent in certain populations, in particular in low- and middle-income regions. The detailed molecular features of TNBC in these regions remain unexplored as samples are mostly accessible as formalin-fixed paraffin embedded (FFPE) archived tissues, a challenging material for advanced genomic and transcriptomic studies. Using dedicated reagents and analysis pipelines, we performed whole exome sequencing and miRNA and mRNA profiling of 12 FFPE tumor tissues collected from pathological archives in Mexico. Sequencing analyses of the tumor tissues and their blood pairs identified TP53 and RB1 genes as the most frequently mutated genes, with a somatic mutation load of 1.7 mutations/exome Mb on average. Transcriptional analyses revealed an overexpression of growth-promoting signals (EGFR, PDGFR, VEGF, PIK3CA, FOXM1), a repression of cell cycle control pathways (TP53, RB1), a deregulation of DNA-repair pathways, and alterations in epigenetic modifiers through miRNA:mRNA network de-regulation. The molecular programs identified were typical of those described in basal-like tumors in other populations. This work demonstrates the feasibility of using archived clinical samples for advanced integrated genomics analyses. It thus opens up opportunities for investigating molecular features of tumors from regions where only FFPE tissues are available, allowing retrospective studies on the search for treatment strategies or on the exploration of the geographic diversity of breast cancer.
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Affiliation(s)
- Felipe Vaca-Paniagua
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, México D.F., México
- Unidad de Biomedicina, FES-Iztacala, Universidad Nacional Autónoma de México (UNAM), México D.F., México
| | - Rosa María Alvarez-Gomez
- Unidad de Genómica y Secuenciación Masiva (UGESEM), Instituto Nacional de Cancerología, México D.F., México
| | | | - Carlos Pérez-Plasencia
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, México D.F., México
- Unidad de Biomedicina, FES-Iztacala, Universidad Nacional Autónoma de México (UNAM), México D.F., México
- Unidad de Genómica y Secuenciación Masiva (UGESEM), Instituto Nacional de Cancerología, México D.F., México
| | - Veronica Fragoso-Ontiveros
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, México D.F., México
- Unidad de Genómica y Secuenciación Masiva (UGESEM), Instituto Nacional de Cancerología, México D.F., México
| | | | - Luis Alonso Herrera
- Unidad de Investigaciones Biomédicas en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México D.F., México
| | - David Cantú
- Unidad de Investigaciones Biomédicas en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), México D.F., México
| | - Enrique Bargallo-Rocha
- Departamento de Tumores Mamarios, Instituto Nacional de Cancerología, México D.F., México
| | - Alejandro Mohar
- Departamento de Epidemiología, Instituto Nacional de Cancerología, México D.F., México
| | - Geoffroy Durand
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Nathalie Forey
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Catherine Voegele
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Maxime Vallée
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Florence Le Calvez-Kelm
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - James McKay
- Group of Genetic Cancer Susceptibility, International Agency for Research on Cancer, Lyon, France
| | - Maude Ardin
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
| | - Stéphanie Villar
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
| | - Jiri Zavadil
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
| | - Magali Olivier
- Group of Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, Lyon, France
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Nsengimana J, Laye J, Filia A, Walker C, Jewell R, Van den Oord JJ, Wolter P, Patel P, Sucker A, Schadendorf D, Jönsson GB, Bishop DT, Newton-Bishop J. Independent replication of a melanoma subtype gene signature and evaluation of its prognostic value and biological correlates in a population cohort. Oncotarget 2015; 6:11683-93. [PMID: 25871393 PMCID: PMC4484486 DOI: 10.18632/oncotarget.3549] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/10/2015] [Indexed: 12/05/2022] Open
Abstract
Development and validation of robust molecular biomarkers has so far been limited in melanoma research. In this paper we used a large population-based cohort to replicate two published gene signatures for melanoma classification. We assessed the signatures prognostic value and explored their biological significance by correlating them with factors known to be associated with survival (vitamin D) or etiological routes (nevi, sun sensitivity and telomere length). Genomewide microarray gene expressions were profiled in 300 archived tumors (224 primaries, 76 secondaries). The two gene signatures classified up to 96% of our samples and showed strong correlation with melanoma specific survival (P=3 x 10(-4)), Breslow thickness (P=5 x 10(-10)), ulceration (P=9.x10-8) and mitotic rate (P=3 x 10(-7)), adding prognostic value over AJCC stage (adjusted hazard ratio 1.79, 95%CI 1.13-2.83), as previously reported. Furthermore, molecular subtypes were associated with season-adjusted serum vitamin D at diagnosis (P=0.04) and genetically predicted telomere length (P=0.03). Specifically, molecular high-grade tumors were more frequent in patients with lower vitamin D levels whereas high immune tumors came from patients with predicted shorter telomeres. Our data confirm the utility of molecular biomarkers in melanoma prognostic estimation using tiny archived specimens and shed light on biological mechanisms likely to impact on cancer initiation and progression.
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Affiliation(s)
- Jérémie Nsengimana
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Jon Laye
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Anastasia Filia
- National Heart and Lung Institute, Imperial College, London, UK
| | - Christy Walker
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Rosalyn Jewell
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Joost J Van den Oord
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
- European Organisation for Research and Treatment of Cancer (EORTC) Melanoma Group, Brussels, Belgium
| | - Pascal Wolter
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Poulam Patel
- School of Medicine, University of Nottingham, Nottingham, UK
- European Organisation for Research and Treatment of Cancer (EORTC) Melanoma Group, Brussels, Belgium
| | - Antje Sucker
- Department of Dermatology, Essen University Hospital, Essen, and German Consortium of Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Dirk Schadendorf
- Department of Dermatology, Essen University Hospital, Essen, and German Consortium of Translational Cancer Research (DKTK), Heidelberg, Germany
- European Organisation for Research and Treatment of Cancer (EORTC) Melanoma Group, Brussels, Belgium
| | - Göran B Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - D. Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
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Xiao Y, Sheng ZM, Taubenberger JK. Isolating Viral and Host RNA Sequences from Archival Material and Production of cDNA Libraries for High-Throughput DNA Sequencing. ACTA ACUST UNITED AC 2015; 37:1E.8.1-16. [PMID: 26344216 DOI: 10.1002/9780471729259.mc01e08s37] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The vast majority of surgical biopsy and post-mortem tissue samples are formalin-fixed and paraffin-embedded (FFPE), but this process leads to RNA degradation that limits gene expression analysis. As an example, the viral RNA genome of the 1918 pandemic influenza A virus was previously determined in a 9-year effort by overlapping RT-PCR from post-mortem samples. Using the protocols described here, the full genome of the 1918 virus was determined at high coverage in one high-throughput sequencing run of a cDNA library derived from total RNA of a 1918 FFPE sample after duplex-specific nuclease treatments. This basic methodological approach should assist in the analysis of FFPE tissue samples isolated over the past century from a variety of infectious diseases.
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Affiliation(s)
- Yongli Xiao
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Zong-Mei Sheng
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jeffery K Taubenberger
- Viral Pathogenesis and Evolution Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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Greytak SR, Engel KB, Bass BP, Moore HM. Accuracy of Molecular Data Generated with FFPE Biospecimens: Lessons from the Literature. Cancer Res 2015; 75:1541-7. [PMID: 25836717 DOI: 10.1158/0008-5472.can-14-2378] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/22/2014] [Indexed: 12/15/2022]
Abstract
Formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens are a valuable resource for molecular cancer research. Although much can be gained from their use, it remains unclear whether the genomic and expression profiles obtained from FFPE biospecimens accurately reflect the physiologic condition of the patient from which they were procured, or if such profiles are confounded by biologic effects from formalin fixation and processing. To assess the physiologic accuracy of genomic and expression data generated with FFPE specimens, we surveyed the literature for articles investigating genomic and expression endpoints in case-matched FFPE and fresh or frozen human biospecimens using the National Cancer Institute's Biospecimen Research Database (http://biospecimens.cancer.gov/brd). Results of the survey revealed that the level of concordance between differentially preserved biospecimens varied among analytical parameters and platforms but also among reports, genes/transcripts of interest, and tumor status. The identified analytical techniques and parameters that resulted in strong correlations between FFPE and frozen biospecimens may provide guidance when optimizing molecular protocols for FFPE use; however, discrepancies reported for similar assays also illustrate the importance of validating protocols optimized for use with FFPE specimens with a case-matched fresh or frozen cohort for each platform, gene or transcript, and FFPE processing regime. On the basis of evidence published to date, validation of analytical parameters with a properly handled frozen cohort is necessary to ensure a high degree of concordance and confidence in the results obtained with FFPE biospecimens.
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Affiliation(s)
| | | | | | - Helen M Moore
- Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland.
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Mansfield AS, Wang L, Cunningham JM, Jen J, Kolbert CP, Sun Z, Yang P. DNA methylation and RNA expression profiles in lung adenocarcinomas of never-smokers. Cancer Genet 2014; 208:253-60. [PMID: 25650174 DOI: 10.1016/j.cancergen.2014.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 12/18/2014] [Accepted: 12/23/2014] [Indexed: 10/24/2022]
Abstract
Lung cancer occurs in never-smokers. Epigenetic changes in lung cancer potentially represent important diagnostic, prognostic, and therapeutic targets. We compared DNA methylation profiles of 28 adenocarcinomas of the lungs of never-smokers with paired adjacent nonmalignant lung tissue. We correlated differential methylation changes with gene expression changes from the same 28 sample pairs. Using principal component analysis, we observed a distinct separation in methylation profiles between tumor and adjacent nonmalignant lung tissue. Tumors were generally hypomethylated compared with adjacent nonmalignant tissue. Of 1,906 CpG sites differentially methylated between tumor and nonmalignant tissue, 1,198 were within classically defined CpG islands where tumors were hypermethylated compared with nonmalignant tissue. A total of 708 sites were outside CpG islands where tumors were hypomethylated compared with nonmalignant tissue. There were significant differences in expression of 351 genes (23%) of the 1,522 genes matched to the differentially methylated CpG sites. Genes that were not significantly differentially expressed and were hypermethylated within CpG sites were enriched for homeobox genes. These results suggest that the methylation profiles of lung adenocarcinomas of never-smokers and adjacent nonmalignant lung tissue are significantly different. Despite the differential methylation of homeobox genes, no significant changes in expression of these genes were detected.
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Affiliation(s)
- Aaron S Mansfield
- Division of Medical Oncology, Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Liang Wang
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Julie M Cunningham
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Medical Genome Facility, Mayo Clinic, Rochester, MN, USA
| | - Jin Jen
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA; Medical Genome Facility, Mayo Clinic, Rochester, MN, USA; Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Zhifu Sun
- Division of Biomedical Statistics and Informatics, Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ping Yang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA; Division of Epidemiology and Department of Medical Genetics, Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
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Royse KE, Zhi D, Conner MG, Clodfelder-Miller B, Srinivasasainagendra V, Vaughan LK, Skibola CF, Crossman DK, Levy S, Shrestha S. Differential Gene Expression Landscape of Co-Existing Cervical Pre-Cancer Lesions Using RNA-seq. Front Oncol 2014; 4:339. [PMID: 25505737 PMCID: PMC4244708 DOI: 10.3389/fonc.2014.00339] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/11/2014] [Indexed: 01/08/2023] Open
Abstract
Genetic changes occurring in different stages of pre-cancer lesions reflect causal events initiating and promoting the progression to cancer. Co-existing pre-cancerous lesions including low- and high-grade squamous intraepithelial lesion (LGSIL and HGSIL), and adjacent “normal” cervical epithelium from six formalin-fixed paraffin-embedded samples were selected. Tissues from these 18 samples were isolated using laser-capture microdissection, RNA was extracted and sequenced. RNA-sequencing generated 2.4 billion raw reads in 18 samples, of which ~50.1% mapped to known and annotated genes in the human genome. There were 40 genes up-regulated and 3 down-regulated (normal to LGSIL) in at least one-third of the sample pairs (same direction and FDR p < 0.05) including S100A7 and KLK6. Previous studies have shown that S110A7 and KLK7 are up-regulated in several other cancers, whereas CCL18, CFTR, and SLC6A14, also differentially expressed in two samples, are up-regulated specifically in cervical cancer. These differentially expressed genes in normal to LGSIL progression were enriched in pathways related to epithelial cell differentiation, keratinocyte differentiation, peptidase, and extracellular activities. In progression from LGSIL to HGSIL, two genes were up-regulated and five down-regulated in at least two samples. Further investigations using co-existing samples, which account for all internal confounders, will provide insights to better understand progression of cervical pre-cancer.
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Affiliation(s)
- Kathryn E Royse
- Department of Epidemiology, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Degui Zhi
- Department of Biostatistics, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Michael G Conner
- Department of Pathology, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Buffie Clodfelder-Miller
- Cellular and Molecular Neuropathology Core, University of Alabama at Birmingham , Birmingham, AL , USA
| | | | - Laura Kelly Vaughan
- Department of Biostatistics, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Christine F Skibola
- Department of Epidemiology, University of Alabama at Birmingham , Birmingham, AL , USA
| | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Shawn Levy
- Hudson Alpha Institute for Biotechnology , Huntsville, AL , USA
| | - Sadeep Shrestha
- Department of Epidemiology, University of Alabama at Birmingham , Birmingham, AL , USA
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Fina E, Callari M, Reduzzi C, D'Aiuto F, Mariani G, Generali D, Pierotti MA, Daidone MG, Cappelletti V. Gene expression profiling of circulating tumor cells in breast cancer. Clin Chem 2014; 61:278-89. [PMID: 25411184 DOI: 10.1373/clinchem.2014.229476] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Determining the transcriptional profile of circulating tumor cells (CTCs) may allow the acquisition of clinically relevant information while overcoming tumor heterogeneity-related biases associated with use of tissue samples for biomarker assessment. However, such molecular characterization is challenging because CTCs are rare and outnumbered by blood cells. METHODS Here, we describe a technical protocol to measure the expression of >29 000 genes in CTCs captured from whole blood with magnetic beads linked with antibodies against epithelial cell adhesion molecule (EpCAM) and the carcinoma-associated mucin, MUC1, designed to be used for CTC characterization in clinical samples. Low numbers of cells (5-200) from the MCF7 and MDA-MB-468 breast cancer cell lines were spiked in healthy donor blood samples and isolated with the AdnaTest EMT-1/Stem CellSelect kit. Gene expression profiles (GEPs) were obtained with the WG-DASL HT assay and compared with GEPs obtained from RNA isolated from cultured cell lines and unspiked samples. RESULTS GEPs from samples containing 25 or more spiked cells correlated (r = 0.95) with cognate 100-ng RNA input samples, clustered separately from blood control samples, and allowed MCF7 and MDA-MB-468 cells to be distinguished. GEPs with comparable technical quality were also obtained in a preliminary series of clinical samples. CONCLUSIONS Our approach allows technically reliable GEPs to be obtained from isolated CTCs for the acquisition of biologically useful information. It is reproducible and suitable for application in prospective studies to assess the clinical utility of CTC GEPs, provided that >25 CTCs can be isolated.
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Affiliation(s)
- Emanuela Fina
- Biomarkers Unit, Department of Experimental Oncology and Molecular Medicine
| | - Maurizio Callari
- Biomarkers Unit, Department of Experimental Oncology and Molecular Medicine
| | - Carolina Reduzzi
- Biomarkers Unit, Department of Experimental Oncology and Molecular Medicine
| | - Francesca D'Aiuto
- Biomarkers Unit, Department of Experimental Oncology and Molecular Medicine
| | | | - Daniele Generali
- U.O. Multidisciplinare di Patologia Mammaria, U.S. Terapia Molecolare e Farmacogenomica, A.O. Istituti Ospitalieri di Cremona, Cremona, Italy
| | - Marco A Pierotti
- Scientific Directorate, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maria G Daidone
- Biomarkers Unit, Department of Experimental Oncology and Molecular Medicine,
| | - Vera Cappelletti
- Biomarkers Unit, Department of Experimental Oncology and Molecular Medicine
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Pathogenetic and diagnostic significance of microRNA deregulation in peripheral T-cell lymphoma not otherwise specified. Blood Cancer J 2014; 4:259. [PMID: 25382608 PMCID: PMC4335255 DOI: 10.1038/bcj.2014.78] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 09/18/2014] [Indexed: 12/14/2022] Open
Abstract
Peripheral T-cell lymphomas not otherwise specified (PTCLs/NOS) are rare and aggressive tumours whose molecular pathogenesis and diagnosis are still challenging. The microRNA (miRNA) profile of 23 PTCLs/NOS was generated and compared with that of normal T-lymphocytes (CD4+, CD8+, naive, activated). The differentially expressed miRNA signature was compared with the gene expression profile (GEP) of the same neoplasms. The obtained gene patterns were tested in an independent cohort of PTCLs/NOS. The miRNA profile of PTCLs/NOS then was compared with that of 10 angioimmunoblastic T-cell lymphomas (AITLs), 6 anaplastic large-cell lymphomas (ALCLs)/ALK+ and 6 ALCLs/ALK−. Differentially expressed miRNAs were validated in an independent set of 20 PTCLs/NOS, 20 AITLs, 19 ALCLs/ALK− and 15 ALCLs/ALK+. Two hundred and thirty-six miRNAs were found to differentiate PTCLs/NOS from activated T-lymphocytes. To assess which miRNAs impacted on GEP, a multistep analysis was performed, which identified all miRNAs inversely correlated to different potential target genes. One of the most discriminant miRNAs was selected and its expression was found to affect the global GEP of the tumours. Moreover, two sets of miRNAs were identified distinguishing PTCL/NOS from AITL and ALCL/ALK−, respectively. The diagnostic accuracy of this tool was very high (83.54%) and its prognostic value validated.
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Auerbach SS, Phadke DP, Mav D, Holmgren S, Gao Y, Xie B, Shin JH, Shah RR, Merrick BA, Tice RR. RNA-Seq-based toxicogenomic assessment of fresh frozen and formalin-fixed tissues yields similar mechanistic insights. J Appl Toxicol 2014; 35:766-80. [DOI: 10.1002/jat.3068] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/22/2014] [Accepted: 07/26/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Scott S. Auerbach
- Biomolecular Screening Branch, Division of the National Toxicology Program; National Institute of Environmental Health Sciences; Research Triangle Park NC 27709 USA
| | | | | | - Stephanie Holmgren
- Library & Information Services Branch, Office of the Deputy Director; National Institute of Environmental Health Sciences; Research Triangle Park NC 27709 USA
| | - Yuan Gao
- Department of Biomedical Engineering; Johns Hopkins University; Baltimore MD 21205 USA
| | - Bin Xie
- Department of Biomedical Engineering; Johns Hopkins University; Baltimore MD 21205 USA
| | - Joo Heon Shin
- Department of Biomedical Engineering; Johns Hopkins University; Baltimore MD 21205 USA
| | | | - B. Alex Merrick
- Biomolecular Screening Branch, Division of the National Toxicology Program; National Institute of Environmental Health Sciences; Research Triangle Park NC 27709 USA
| | - Raymond R. Tice
- Biomolecular Screening Branch, Division of the National Toxicology Program; National Institute of Environmental Health Sciences; Research Triangle Park NC 27709 USA
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35
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Konecny GE, Wang C, Hamidi H, Winterhoff B, Kalli KR, Dering J, Ginther C, Chen HW, Dowdy S, Cliby W, Gostout B, Podratz KC, Keeney G, Wang HJ, Hartmann LC, Slamon DJ, Goode EL. Prognostic and therapeutic relevance of molecular subtypes in high-grade serous ovarian cancer. J Natl Cancer Inst 2014. [PMID: 25269487 DOI: 10.1093/jnci/dju249]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Molecular classification of high-grade serous ovarian cancer (HGSOC) using transcriptional profiling has proven to be complex and difficult to validate across studies. We determined gene expression profiles of 174 well-annotated HGSOCs and demonstrate prognostic significance of the prespecified TCGA Network gene signatures. Furthermore, we confirm the presence of four HGSOC transcriptional subtypes using a de novo classification. Survival differed statistically significantly between de novo subtypes (log rank, P = .006) and was the best for the immunoreactive-like subtype, but statistically significantly worse for the proliferative- or mesenchymal-like subtypes (adjusted hazard ratio = 1.89, 95% confidence interval = 1.18 to 3.02, P = .008, and adjusted hazard ratio = 2.45, 95% confidence interval = 1.43 to 4.18, P = .001, respectively). More prognostic information was provided by the de novo than the TCGA classification (Likelihood Ratio tests, P = .003 and P = .04, respectively). All statistical tests were two-sided. These findings were replicated in an external data set of 185 HGSOCs and confirm the presence of four prognostically relevant molecular subtypes that have the potential to guide therapy decisions.
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Affiliation(s)
- Gottfried E Konecny
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Chen Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Habib Hamidi
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Boris Winterhoff
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Kimberly R Kalli
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Judy Dering
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Charles Ginther
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Hsiao-Wang Chen
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Sean Dowdy
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - William Cliby
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Bobbie Gostout
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Karl C Podratz
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Gary Keeney
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - He-Jing Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Lynn C Hartmann
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Dennis J Slamon
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Ellen L Goode
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
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Ghatak S, Sanga Z, Pautu JL, Kumar NS. Coextraction and PCR Based Analysis of Nucleic Acids From Formalin-Fixed Paraffin-Embedded Specimens. J Clin Lab Anal 2014; 29:485-92. [PMID: 25277467 DOI: 10.1002/jcla.21798] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 05/12/2014] [Accepted: 08/07/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Retrospective studies of archived human specimens, with known clinical follow-up, are used to identify predictive and prognostic molecular markers of disease. Due to biochemical differences, however, formalin-fixed paraffin embedded (FFPE) DNA and RNA have generally been extracted separately from either different tissue sections or from the same section by dividing the digested tissue. Our optimized co-extraction approach provides the option of collecting DNA, which would otherwise be discarded or degraded, for additional or subsequent studies because of the high importance and less availability of clinical FFPE specimen. METHODS Coextraction of DNA and RNA from a single gastric cancer FFPE specimen was optimized by using TRIzol and purifying DNA from the lower aqueous and RNA from the upper organic phases. The protocol involves modification of incubation period for 30 min with proteinase K in glycin-tris-ethylenediamine tetra acetic acid buffer before adding TRIzol. RESULTS All samples tested successfully performed semiquantitative gene expression by reverse transcriptase PCR. The quantity and quality of DNA from FFPE samples was high which resulted in successful PCR amplification. The isolated DNA also aided in detection of Helicobacter pylori by amplifying the ribosomal 16S gene in a multiplex PCR reaction along with cagA. CONCLUSION These results show that the RNA/DNA isolated by this method can be used for easy clinical diagnosis of disease-related gene expression as well as mutation and pathogen detection from a homogenous population of tumor cells.
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Affiliation(s)
- Souvik Ghatak
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, India
| | - Zothan Sanga
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, India
| | - Jeremy L Pautu
- Mizoram State Cancer Institute, Zemabawk, Aizawl, Mizoram, India
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37
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Konecny GE, Wang C, Hamidi H, Winterhoff B, Kalli KR, Dering J, Ginther C, Chen HW, Dowdy S, Cliby W, Gostout B, Podratz KC, Keeney G, Wang HJ, Hartmann LC, Slamon DJ, Goode EL. Prognostic and therapeutic relevance of molecular subtypes in high-grade serous ovarian cancer. J Natl Cancer Inst 2014. [PMID: 25269487 DOI: 10.1093/jnci/dju249.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Molecular classification of high-grade serous ovarian cancer (HGSOC) using transcriptional profiling has proven to be complex and difficult to validate across studies. We determined gene expression profiles of 174 well-annotated HGSOCs and demonstrate prognostic significance of the prespecified TCGA Network gene signatures. Furthermore, we confirm the presence of four HGSOC transcriptional subtypes using a de novo classification. Survival differed statistically significantly between de novo subtypes (log rank, P = .006) and was the best for the immunoreactive-like subtype, but statistically significantly worse for the proliferative- or mesenchymal-like subtypes (adjusted hazard ratio = 1.89, 95% confidence interval = 1.18 to 3.02, P = .008, and adjusted hazard ratio = 2.45, 95% confidence interval = 1.43 to 4.18, P = .001, respectively). More prognostic information was provided by the de novo than the TCGA classification (Likelihood Ratio tests, P = .003 and P = .04, respectively). All statistical tests were two-sided. These findings were replicated in an external data set of 185 HGSOCs and confirm the presence of four prognostically relevant molecular subtypes that have the potential to guide therapy decisions.
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Affiliation(s)
- Gottfried E Konecny
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Chen Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Habib Hamidi
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Boris Winterhoff
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Kimberly R Kalli
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Judy Dering
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Charles Ginther
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Hsiao-Wang Chen
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Sean Dowdy
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - William Cliby
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Bobbie Gostout
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Karl C Podratz
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Gary Keeney
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - He-Jing Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Lynn C Hartmann
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Dennis J Slamon
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Ellen L Goode
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
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Konecny GE, Wang C, Hamidi H, Winterhoff B, Kalli KR, Dering J, Ginther C, Chen HW, Dowdy S, Cliby W, Gostout B, Podratz KC, Keeney G, Wang HJ, Hartmann LC, Slamon DJ, Goode EL. Prognostic and therapeutic relevance of molecular subtypes in high-grade serous ovarian cancer. J Natl Cancer Inst 2014. [PMID: 25269487 DOI: 10.1093/jnci/dju249] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Molecular classification of high-grade serous ovarian cancer (HGSOC) using transcriptional profiling has proven to be complex and difficult to validate across studies. We determined gene expression profiles of 174 well-annotated HGSOCs and demonstrate prognostic significance of the prespecified TCGA Network gene signatures. Furthermore, we confirm the presence of four HGSOC transcriptional subtypes using a de novo classification. Survival differed statistically significantly between de novo subtypes (log rank, P = .006) and was the best for the immunoreactive-like subtype, but statistically significantly worse for the proliferative- or mesenchymal-like subtypes (adjusted hazard ratio = 1.89, 95% confidence interval = 1.18 to 3.02, P = .008, and adjusted hazard ratio = 2.45, 95% confidence interval = 1.43 to 4.18, P = .001, respectively). More prognostic information was provided by the de novo than the TCGA classification (Likelihood Ratio tests, P = .003 and P = .04, respectively). All statistical tests were two-sided. These findings were replicated in an external data set of 185 HGSOCs and confirm the presence of four prognostically relevant molecular subtypes that have the potential to guide therapy decisions.
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Affiliation(s)
- Gottfried E Konecny
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Chen Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Habib Hamidi
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Boris Winterhoff
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Kimberly R Kalli
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Judy Dering
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Charles Ginther
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Hsiao-Wang Chen
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Sean Dowdy
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - William Cliby
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Bobbie Gostout
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Karl C Podratz
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Gary Keeney
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - He-Jing Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Lynn C Hartmann
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Dennis J Slamon
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Ellen L Goode
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
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Konecny GE, Wang C, Hamidi H, Winterhoff B, Kalli KR, Dering J, Ginther C, Chen HW, Dowdy S, Cliby W, Gostout B, Podratz KC, Keeney G, Wang HJ, Hartmann LC, Slamon DJ, Goode EL. Prognostic and therapeutic relevance of molecular subtypes in high-grade serous ovarian cancer. J Natl Cancer Inst 2014; 106:dju249. [PMID: 25269487 DOI: 10.1093/jnci/dju249] [Citation(s) in RCA: 262] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Molecular classification of high-grade serous ovarian cancer (HGSOC) using transcriptional profiling has proven to be complex and difficult to validate across studies. We determined gene expression profiles of 174 well-annotated HGSOCs and demonstrate prognostic significance of the prespecified TCGA Network gene signatures. Furthermore, we confirm the presence of four HGSOC transcriptional subtypes using a de novo classification. Survival differed statistically significantly between de novo subtypes (log rank, P = .006) and was the best for the immunoreactive-like subtype, but statistically significantly worse for the proliferative- or mesenchymal-like subtypes (adjusted hazard ratio = 1.89, 95% confidence interval = 1.18 to 3.02, P = .008, and adjusted hazard ratio = 2.45, 95% confidence interval = 1.43 to 4.18, P = .001, respectively). More prognostic information was provided by the de novo than the TCGA classification (Likelihood Ratio tests, P = .003 and P = .04, respectively). All statistical tests were two-sided. These findings were replicated in an external data set of 185 HGSOCs and confirm the presence of four prognostically relevant molecular subtypes that have the potential to guide therapy decisions.
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Affiliation(s)
- Gottfried E Konecny
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Chen Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Habib Hamidi
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Boris Winterhoff
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Kimberly R Kalli
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Judy Dering
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Charles Ginther
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Hsiao-Wang Chen
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Sean Dowdy
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - William Cliby
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Bobbie Gostout
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Karl C Podratz
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Gary Keeney
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - He-Jing Wang
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Lynn C Hartmann
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Dennis J Slamon
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
| | - Ellen L Goode
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (GEK, HH, JD, CG, HWC, DJS); Department of Health Sciences Research (CW, ELG), Department of Gynecologic Surgery (BW, SD, WC, BG, KCP), Department of Medicine (KRK, LCH), and Department of Pathology (GK), Mayo Clinic, Rochester, MN; Department of Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA (HJW)
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van Galen P, Kreso A, Wienholds E, Laurenti E, Eppert K, Lechman ER, Mbong N, Hermans K, Dobson S, April C, Fan JB, Dick JE. Reduced lymphoid lineage priming promotes human hematopoietic stem cell expansion. Cell Stem Cell 2014; 14:94-106. [PMID: 24388174 DOI: 10.1016/j.stem.2013.11.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 10/07/2013] [Accepted: 11/25/2013] [Indexed: 01/10/2023]
Abstract
The hematopoietic system sustains regeneration throughout life by balancing self-renewal and differentiation. To stay poised for mature blood production, hematopoietic stem cells (HSCs) maintain low-level expression of lineage-associated genes, a process termed lineage priming. Here, we modulated expression levels of Inhibitor of DNA binding (ID) proteins to ask whether lineage priming affects self-renewal of human HSCs. We found that lentiviral overexpression of ID proteins in cord blood HSCs biases myeloerythroid commitment at the expense of lymphoid differentiation. Conversely, reducing ID2 expression levels increases lymphoid potential. Mechanistically, ID2 inhibits the transcription factor E47 to attenuate B-lymphoid priming in HSCs and progenitors. Strikingly, ID2 overexpression also results in a 10-fold expansion of HSCs in serial limiting dilution assays, indicating that early lymphoid transcription factors antagonize human HSC self-renewal. The relationship between lineage priming and self-renewal can be exploited to increase expansion of transplantable human HSCs and points to broader implications for other stem cell populations.
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Affiliation(s)
- Peter van Galen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Antonija Kreso
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Erno Wienholds
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Elisa Laurenti
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Kolja Eppert
- Department of Pediatrics, McGill University and the Research Institute of the McGill University Health Centre, Westmount, QC H3Z 2Z3, Canada
| | - Eric R Lechman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Nathan Mbong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Karin Hermans
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Stephanie Dobson
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | | | | | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1L7, Canada.
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Christophi GP, Caza T, Curtiss C, Gumber D, Massa PT, Landas SK. Gene expression profiles in granuloma tissue reveal novel diagnostic markers in sarcoidosis. Exp Mol Pathol 2014; 96:393-9. [PMID: 24768588 DOI: 10.1016/j.yexmp.2014.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 04/10/2014] [Indexed: 01/16/2023]
Abstract
Sarcoidosis is an immune-mediated multisystem disease characterized by the formation of non-caseating granulomas. The pathogenesis of sarcoidosis is unclear, with proposed infectious or environmental antigens triggering an aberrant immune response in susceptible hosts. Multiple pro-inflammatory signaling pathways have been implicated in mediating macrophage activation and granuloma formation in sarcoidosis, including IFN-γ/STAT-1, IL-6/STAT-3, and NF-κB. It is difficult to distinguish sarcoidosis from other granulomatous diseases or assess disease severity and treatment response with histopathology alone. Therefore, development of improved diagnostic tools is imperative. Herein, we describe an efficient and reliable technique to classify granulomatous disease through selected gene expression and identify novel genes and cytokine pathways contributing to the pathogenesis of sarcoidosis. We quantified the expression of twenty selected mRNAs extracted from formalin-fixed paraffin embedded (FFPE) tissue (n = 38) of normal lung, suture granulomas, sarcoid granulomas, and fungal granulomas. Utilizing quantitative real-time RT-PCR we analyzed the expression of several genes, including IL-6, COX-2, MCP-1, IFN-γ, T-bet, IRF-1, Nox2, IL-33, and eotaxin-1 and revealed differential regulation between suture, sarcoidosis, and fungal granulomas. This is the first study demonstrating that quantification of target gene expression in FFPE tissue biopsies is a potentially effective diagnostic and research tool in sarcoidosis.
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Affiliation(s)
- George P Christophi
- Department of Gastroenterology, Washington University School of Medicine, St. Louis, MO, United States.
| | - Tiffany Caza
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Christopher Curtiss
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Divya Gumber
- Department of Internal Medicine, Cleveland Clinic, Cleveland, OH, United States
| | - Paul T Massa
- Department of Microbiology & Immunology, SUNY Upstate Medical University, Syracuse, NY, United States
| | - Steve K Landas
- Department of Pathology, SUNY Upstate Medical University, Syracuse, NY, United States
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Pentheroudakis G, Kotoula V, Fountzilas E, Kouvatseas G, Basdanis G, Xanthakis I, Makatsoris T, Charalambous E, Papamichael D, Samantas E, Papakostas P, Bafaloukos D, Razis E, Christodoulou C, Varthalitis I, Pavlidis N, Fountzilas G. A study of gene expression markers for predictive significance for bevacizumab benefit in patients with metastatic colon cancer: a translational research study of the Hellenic Cooperative Oncology Group (HeCOG). BMC Cancer 2014; 14:111. [PMID: 24555920 PMCID: PMC3933361 DOI: 10.1186/1471-2407-14-111] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 02/11/2014] [Indexed: 01/08/2023] Open
Abstract
Background Bevacizumab, an antibody neutralizing Vascular Endothelial Growth Factor (VEGF), is licensed for the management of patients with advanced colon cancer. However, tumor biomarkers identifying the molecular tumor subsets most amenable to angiogenesis modulation are lacking. Methods We profiled expession of 24526 genes by means of whole genome 24 K DASL (c-DNA-mediated, Annealing, Selection and Ligation) arrays, (Illumina, CA) in 16 bevacizumab-treated patients with advanced colon cancer (Test set). Genes with correlation to 8-month Progression-free status were studied by means of qPCR in two independent colon cancer cohorts: 49 patients treated with bevacizumab + chemotherapy (Bevacizumab qPCR set) and 72 patients treated with chemotherapy only (Control qPCR set). Endpoints were best tumor response before metastasectomy (ORR) and progression-free survival (PFS). Results Five genes were significantly correlated to 8-month progression-free status in the Test set: overexpression of KLF12 and downregulation of AGR2, ALDH6A1, MCM5, TFF2. In the two independent datasets, irinotecan- or oxaliplatin-based chemotherapy was administered as first-line treatment and metastasectomies were subsequently applied in 8-14% of patients. No prognostically significant gene classifier encompassing all five genes could be validated in the Bevacizumab or Control qPCR sets. The complex gene expression profile of all-low tumor (ALDH6A1 + TFF2 + MCM5) was strongly associated with ORR in the Bevacizumab qPCR set (ORR 85.7%, p = 0.007), but not in the Control set (ORR 36.4%, p = 0.747). The Odds Ratio for response for the all-low tumor (ALDH6A1 + TFF2 + MCM5) profile versus any other ALDH6A1 + TFF2 + MCM5 profile was 15 (p = 0.018) in the Bevacizumab qPCR set but only 0.72 (p = 0.63) in the Control set. The tumor expression profile of (KLF12-high + TFF2-low) was significantly associated with PFS only in the Bevacizumab qPCR set: bevacizumab-treated patients with (KLF12-high + TFF2-low) tumors had superior PFS (median 14 months, 95% CI 2-21) compared to patients with any other (KLF12 + TFF2) expression profile (median PFS 7 months, 95% CI 5-10, p = 0.021). The Hazard Ratio for disease progression for (KLF12-high + TFF2-low) versus any other KLF12 + TFF2 expression profile was 2.92 (p = 0.03) in the Validation and 1.29 (p = 0.39) in the Control set. Conclusions Our «three-stage» hypothesis-generating study failed to validate the prognostic significance of a five-gene classifier in mCRC patients. Exploratory analyses suggest two gene signatures that are potentially associated with bevazicumab benefit in patients with advanced colon cancer.
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Kojima K, April C, Canasto-Chibuque C, Chen X, Deshmukh M, Venkatesh A, Tan PS, Kobayashi M, Kumada H, Fan JB, Hoshida Y. Transcriptome profiling of archived sectioned formalin-fixed paraffin-embedded (AS-FFPE) tissue for disease classification. PLoS One 2014; 9:e86961. [PMID: 24498002 PMCID: PMC3907407 DOI: 10.1371/journal.pone.0086961] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 12/19/2013] [Indexed: 01/04/2023] Open
Abstract
Background Archived tissues from previously completed prospective trials represent invaluable resource for biomarker development. However, such specimens are often stored as sections on glass slides, in which RNA is severely degraded due to prolonged air exposure. We evaluated whether a proportion of archived sectioned formalin-fixed paraffin-embedded (AS-FFPE) tissues yield transcriptome profiles comparable to freshly cut (FC) FFPE tissues, which can be used for retrospective class prediction analysis. Methods Genome-wide transcriptome profiles of 6 to 7-year-old AS-FFPE tissue sections (generated from 5 to 16-year-old blocks) of 83 hepatocellular carcinoma (HCC) and 47 liver cirrhosis samples were generated by using whole-genome DASL assay (Illumina) and digital transcript counting (nCounter) assay (NanoString), and gene signature-based prediction of HCC subclasses and prognosis was compared with previously generated FC-FFPE profiles from the same tissue blocks. Results RNA quality and assay reproducibility of AS-FFPE RNA were comparable to intermediate to poor quality FC-FFPE samples (RNA Integrity Number: up to 2.50, R-square for technical replicates: up to 0.93). Analyzable transcriptome profiles were obtained in 64 (77%) HCC and 36 (77%) cirrhosis samples. Statistically more confident predictions based on random resampling-based method (nearest template prediction) were obtained in 37 (58%) HCC and 13 (36%) cirrhosis samples. Predictions made in FC-FFPE profiles were reproduced in 36 (97%) HCC and 11 (85%) cirrhosis AS-FFPE profiles. nCounter assay was tested in 24 cirrhosis samples, which yielded confident prediction in 15 samples (63%), of which 10 samples (67%) showed concordant predictions with FC-FFPE profiles. Conclusions AS-FFPE tissues yielded poorer quality RNA and transcriptome profiles compared to FC-FFPE tissues. Statistically more confident class prediction was feasible in 37 of 83 HCC samples and 13 of 47 cirrhosis samples. These results suggest that AS-FFPE tissues can be regarded as a resource for retrospective transcriptome-based class prediction analysis when they are the only available materials.
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Affiliation(s)
- Kensuke Kojima
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Craig April
- Illumina, Inc., San Diego, California, United States of America
| | - Claudia Canasto-Chibuque
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Xintong Chen
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Manjeet Deshmukh
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Anu Venkatesh
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Poh Seng Tan
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | | | | | - Jian-Bing Fan
- Illumina, Inc., San Diego, California, United States of America
| | - Yujin Hoshida
- Liver Cancer Program, Tisch Cancer Institute, Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail:
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Hatzfeld M, Wolf A, Keil R. Plakophilins in Desmosomal Adhesion and Signaling. ACTA ACUST UNITED AC 2014; 21:25-42. [DOI: 10.3109/15419061.2013.876017] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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45
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Ghosh S, Ashcraft K, Jahid MJ, April C, Ghajar CM, Ruan J, Wang H, Foster M, Hughes DC, Ramirez AG, Huang T, Fan JB, Hu Y, Li R. Regulation of adipose oestrogen output by mechanical stress. Nat Commun 2013; 4:1821. [PMID: 23652009 DOI: 10.1038/ncomms2794] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 03/22/2013] [Indexed: 01/24/2023] Open
Abstract
Adipose stromal cells are the primary source of local oestrogens in adipose tissue, aberrant production of which promotes oestrogen receptor-positive breast cancer. Here we show that extracellular matrix compliance and cell contractility are two opposing determinants for oestrogen output of adipose stromal cells. Using synthetic extracellular matrix and elastomeric micropost arrays with tunable rigidity, we find that increasing matrix compliance induces transcription of aromatase, a rate-limiting enzyme in oestrogen biosynthesis. This mechanical cue is transduced sequentially by discoidin domain receptor 1, c-Jun N-terminal kinase 1, and phosphorylated JunB, which binds to and activates two breast cancer-associated aromatase promoters. In contrast, elevated cell contractility due to actin stress fibre formation dampens aromatase transcription. Mechanically stimulated stromal oestrogen production enhances oestrogen-dependent transcription in oestrogen receptor-positive tumour cells and promotes their growth. This novel mechanotransduction pathway underlies communications between extracellular matrix, stromal hormone output, and cancer cell growth within the same microenvironment.
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Affiliation(s)
- Sagar Ghosh
- Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
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Molecular Signatures of Recurrent Hepatocellular Carcinoma Secondary to Hepatitis C Virus following Liver Transplantation. J Transplant 2013; 2013:878297. [PMID: 24377043 PMCID: PMC3860124 DOI: 10.1155/2013/878297] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/25/2013] [Indexed: 01/12/2023] Open
Abstract
Chronic hepatitis C virus (HCV) induced hepatocellular carcinoma (HCC) is a primary indication for liver transplantation (LT). In western countries, the estimated rate of HCC recurrence following LT is between 15% and 20% and is a major cause of mortality. Currently, there is no standard method to treat patients who are at high risk for HCC recurrence. The aim of this study was to investigate the molecular signatures underlying HCC recurrence that may lead to future studies on gene regulation contributing to new therapeutic options. Two groups of patients were selected, one including patients with HCV who developed HCC recurrence (HCC-R) ≤3 years from LT and the second group including patients with HCV who did not have recurrent HCC (HCC-NR). Microarray analysis containing more than 29,000 known genes was performed on formalin-fixed-paraffin-embedded (FFPE) liver tissue from explanted livers. Gene expression profiling revealed 194 differentially regulated genes between the two groups. These genes belonged to cellular networks including cell cycle G1/S checkpoint regulators, RAN signaling, chronic myeloid leukemia signaling, molecular mechanisms of cancer, FXR/RXR activation and hepatic cholestasis. A subset of molecular signatures associated with HCC recurrence was found. The expression levels of these genes were validated by quantitative PCR analysis.
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Feasibility of RNA and DNA extraction from fresh pipelle and archival endometrial tissues for use in gene expression and SNP arrays. Obstet Gynecol Int 2013; 2013:576842. [PMID: 24282417 PMCID: PMC3825122 DOI: 10.1155/2013/576842] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 08/22/2013] [Indexed: 11/17/2022] Open
Abstract
Identifying molecular markers of endometrial hyperplasia (neoplasia) progression is critical to cancer prevention. To assess RNA and DNA quantity and quality from routinely collected endometrial samples and evaluate the performance of RNA- and DNA-based arrays across endometrial tissue types, we collected fresh frozen (FF) Pipelle, FF curettage, and formalin-fixed paraffin-embedded (FFPE) hysterectomy specimens (benign indications) from eight women. Additionally, neoplastic and uninvolved tissues from 24 FFPE archival hysterectomy specimens with endometrial hyperplasias and carcinomas were assessed. RNA was extracted from 15 of 16 FF and 51 of 51 FFPE samples, with yields >1.2 μg for 13/15 (87%) FF and 50/51 (98%) FFPE samples. Extracted RNA was of high quality; all samples performed successfully on the Illumina whole-genome cDNA-mediated annealing, selection, extension, and ligation (WG-DASL) array and performance did not vary by tissue type. While DNA quantity from FFPE samples was excellent, quality was not sufficient for successful performance on the Affymetrix SNP Array 6.0. In conclusion, FF Pipelle samples, which are minimally invasive, yielded excellent quantity and quality of RNA for gene expression arrays (similar to FF curettage) and should be considered for use in genomic studies. FFPE-derived DNA should be evaluated on new rapidly evolving sequencing platforms.
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Li WQ, Han J, Widlund HR, Correll M, Wang YE, Quackenbush J, Mihm MC, Canales AL, Wu S, Golub T, Hoshida Y, Hunter DJ, Murphy G, Kupper TS, Qureshi AA. CXCR4 pathway associated with family history of melanoma. Cancer Causes Control 2013; 25:125-32. [PMID: 24158781 DOI: 10.1007/s10552-013-0315-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 10/15/2013] [Indexed: 01/24/2023]
Abstract
PURPOSE Genetic predisposition plays a major role in the etiology of melanoma, but known genetic markers only account for a limited fraction of family-history-associated melanoma cases. Expression microarrays have offered the opportunity to identify further genomic profiles correlated with family history of melanoma. We aimed to distinguish mRNA expression signatures between melanoma cases with and without a family history of melanoma. METHODS Based on the Nurses' Health Study, family history was defined as having one or more first-degree family members diagnosed with melanoma. Melanoma diagnosis was confirmed by reviewing pathology reports, and tumor blocks were collected by mail from across the USA. Genomic interrogation was accomplished through evaluating expression profiling of formalin-fixed paraffin-embedded tissues from 78 primary cutaneous invasive melanoma cases, on either a 6K or whole-genome (24K) Illumina gene chip. Gene set enrichment analysis was performed for each batch to determine the differentially enriched pathways and key contributing genes. RESULTS The CXC chemokine receptor 4 (CXCR4) pathway was consistently up-regulated within cases of familial melanoma in both platforms. Leading edge analysis showed four genes from the CXCR4 pathway, including MAPK1, PLCG1, CRK, and PTK2, were among the core members that contributed to the enrichment of this pathway. There was no association between the enrichment of CXCR4 pathway and NRAS, BRAF mutation, or Breslow thickness of the primary melanoma cases. CONCLUSIONS We found that the CXCR4 pathway might constitute a novel susceptibility pathway associated with family history of melanoma in first-degree relatives.
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Affiliation(s)
- Wen-Qing Li
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, 45 Francis St, 221L, Boston, MA, 02115, USA
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Xu W, Banerji S, Davie JR, Kassie F, Yee D, Kratzke R. Yin Yang gene expression ratio signature for lung cancer prognosis. PLoS One 2013; 8:e68742. [PMID: 23874744 PMCID: PMC3714286 DOI: 10.1371/journal.pone.0068742] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 06/03/2013] [Indexed: 01/03/2023] Open
Abstract
Many studies have established gene expression-based prognostic signatures for lung cancer. All of these signatures were built from training data sets by learning the correlation of gene expression with the patients' survival time. They require all new sample data to be normalized to the training data, ultimately resulting in common problems of low reproducibility and impracticality. To overcome these problems, we propose a new signature model which does not involve data training. We hypothesize that the imbalance of two opposing effects in lung cancer cells, represented by Yin and Yang genes, determines a patient's prognosis. We selected the Yin and Yang genes by comparing expression data from normal lung and lung cancer tissue samples using both unsupervised clustering and pathways analyses. We calculated the Yin and Yang gene expression mean ratio (YMR) as patient risk scores. Thirty-one Yin and thirty-two Yang genes were identified and selected for the signature development. In normal lung tissues, the YMR is less than 1.0; in lung cancer cases, the YMR is greater than 1.0. The YMR was tested for lung cancer prognosis prediction in four independent data sets and it significantly stratified patients into high- and low-risk survival groups (p = 0.02, HR = 2.72; p = 0.01, HR = 2.70; p = 0.007, HR = 2.73; p = 0.005, HR = 2.63). It also showed prediction of the chemotherapy outcomes for stage II & III. In multivariate analysis, the YMR risk factor was more successful at predicting clinical outcomes than other commonly used clinical factors, with the exception of tumor stage. The YMR can be measured in an individual patient in the clinic independent of gene expression platform. This study provided a novel insight into the biology of lung cancer and shed light on the clinical applicability.
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Affiliation(s)
- Wayne Xu
- Manitoba Institute of Cell Biology, University of Manitoba, Winnipeg, Canada.
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Piccaluga PP, Fuligni F, De Leo A, Bertuzzi C, Rossi M, Bacci F, Sabattini E, Agostinelli C, Gazzola A, Laginestra MA, Mannu C, Sapienza MR, Hartmann S, Hansmann ML, Piva R, Iqbal J, Chan JC, Weisenburger D, Vose JM, Bellei M, Federico M, Inghirami G, Zinzani PL, Pileri SA. Molecular profiling improves classification and prognostication of nodal peripheral T-cell lymphomas: results of a phase III diagnostic accuracy study. J Clin Oncol 2013; 31:3019-25. [PMID: 23857971 DOI: 10.1200/jco.2012.42.5611] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
PURPOSE The differential diagnosis among the commonest peripheral T-cell lymphomas (PTCLs; ie, PTCL not otherwise specified [NOS], angioimmunoblastic T-cell lymphoma [AITL], and anaplastic large-cell lymphoma [ALCL]) is difficult, with the morphologic and phenotypic features largely overlapping. We performed a phase III diagnostic accuracy study to test the ability of gene expression profiles (GEPs; index test) to identify PTCL subtype. METHODS We studied 244 PTCLs, including 158 PTCLs NOS, 63 AITLs, and 23 ALK-negative ALCLs. The GEP-based classification method was established on a support vector machine algorithm, and the reference standard was an expert pathologic diagnosis according to WHO classification. RESULTS First, we identified molecular signatures (molecular classifier [MC]) discriminating either AITL and ALK-negative ALCL from PTCL NOS in a training set. Of note, the MC was developed in formalin-fixed paraffin-embedded (FFPE) samples and validated in both FFPE and frozen tissues. Second, we found that the overall accuracy of the MC was remarkable: 98% to 77% for AITL and 98% to 93% for ALK-negative ALCL in test and validation sets of patient cases, respectively. Furthermore, we found that the MC significantly improved the prognostic stratification of patients with PTCL. Particularly, it enhanced the distinction of ALK-negative ALCL from PTCL NOS, especially from some CD30+ PTCL NOS with uncertain morphology. Finally, MC discriminated some T-follicular helper (Tfh) PTCL NOS from AITL, providing further evidence that a group of PTCLs NOS shares a Tfh derivation with but is distinct from AITL. CONCLUSION Our findings support the usage of an MC as additional tool in the diagnostic workup of nodal PTCL.
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