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Luo J, Zhang B, Cui L, Liu T, Gu Y. FMO1 gene expression independently predicts favorable recurrence-free survival of classical papillary thyroid cancer. Future Oncol 2019; 15:1303-1311. [PMID: 30757917 DOI: 10.2217/fon-2018-0885] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aim: To examine the expression profile of FMO1 in papillary thyroid cancer (PTC) and its prognostic value in recurrence-free survival (RFS). Methods: A retrospective analysis was performed using data from the Cancer Genome Atlas and Human Protein Atlas. Results: The most frequent variants of PTC had decreased FMO1 expression compared with their respective adjacent normal tissues. However, even under the best cut-off model, high FMO1 expression was only significantly associated with better RFS in classical PTC (p < 0.001), but not in other two variants. High FMO1 expression independently predicted favorable RFS (hazard ratio: 0.202; 95% CI: 0.084-0.487; p < 0.001) in classical PTC. Conclusion: High FMO1 expression might serve as a biomarker that independently predicts favorable RFS in classical PTC patients.
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Affiliation(s)
- Jing Luo
- Department of Breast Surgery, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, University of Electronic Science & Technology of China, Chengdu 610072, Sichuan, PR China
| | - Bowei Zhang
- Department of Vascular & Thyroid Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science & Technology of China, Chengdu 610072, Sichuan, PR China
| | - Likun Cui
- Department of Vascular & Thyroid Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science & Technology of China, Chengdu 610072, Sichuan, PR China
| | - Tong Liu
- Department of Vascular & Thyroid Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science & Technology of China, Chengdu 610072, Sichuan, PR China
| | - Yi Gu
- Department of Vascular & Thyroid Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science & Technology of China, Chengdu 610072, Sichuan, PR China
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2
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Hahn ME, Timme-Laragy AR, Karchner SI, Stegeman JJ. Nrf2 and Nrf2-related proteins in development and developmental toxicity: Insights from studies in zebrafish (Danio rerio). Free Radic Biol Med 2015; 88:275-289. [PMID: 26130508 PMCID: PMC4698826 DOI: 10.1016/j.freeradbiomed.2015.06.022] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/11/2015] [Accepted: 06/15/2015] [Indexed: 12/14/2022]
Abstract
Oxidative stress is an important mechanism of chemical toxicity, contributing to developmental toxicity and teratogenesis as well as to cardiovascular and neurodegenerative diseases and diabetic embryopathy. Developing animals are especially sensitive to effects of chemicals that disrupt the balance of processes generating reactive species and oxidative stress, and those anti-oxidant defenses that protect against oxidative stress. The expression and inducibility of anti-oxidant defenses through activation of NFE2-related factor 2 (Nrf2) and related proteins is an essential process affecting the susceptibility to oxidants, but the complex interactions of Nrf2 in determining embryonic response to oxidants and oxidative stress are only beginning to be understood. The zebrafish (Danio rerio) is an established model in developmental biology and now also in developmental toxicology and redox signaling. Here we review the regulation of genes involved in protection against oxidative stress in developing vertebrates, with a focus on Nrf2 and related cap'n'collar (CNC)-basic-leucine zipper (bZIP) transcription factors. Vertebrate animals including zebrafish share Nfe2, Nrf1, Nrf2, and Nrf3 as well as a core set of genes that respond to oxidative stress, contributing to the value of zebrafish as a model system with which to investigate the mechanisms involved in regulation of redox signaling and the response to oxidative stress during embryolarval development. Moreover, studies in zebrafish have revealed nrf and keap1 gene duplications that provide an opportunity to dissect multiple functions of vertebrate NRF genes, including multiple sensing mechanisms involved in chemical-specific effects.
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Affiliation(s)
- Mark E Hahn
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America.
| | - Alicia R Timme-Laragy
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America; Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Sibel I Karchner
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - John J Stegeman
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
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3
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Yi YW, Oh S. Comparative analysis of NRF2-responsive gene expression in AcPC-1 pancreatic cancer cell line. Genes Genomics 2014; 37:97-109. [PMID: 25540678 PMCID: PMC4269820 DOI: 10.1007/s13258-014-0253-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 11/27/2014] [Indexed: 02/08/2023]
Abstract
NRF2 is a nuclear transcription factor activated in response to oxidative stress and related with metabolizing of xenotoxic materials and ABC transporter mediated drug resistance. We studied the expression of mRNAs under the siRNA-mediated knockdown of NRF2 and tBHQ-treated condition in AsPC-1 metastatic pancreatic cancer cell line to understand the AsPC-1 specific role(s) of NRF2 and further to investigate the relationship between drug resistance and metastatic plasticity and mobility of AsPc1. Here we show that the genes of aldo–keto reductases, cytochrome P450 family, aldehyde dehydrogenase, thioredoxin reductase, ABC transporter and epoxide hydrolase responsible for drug metabolism or oxidative stress concisely responded to NRF2 stabilization and knockdown of NRF2. In addition the expression of PIR, a candidate of oncogene and KISS1, a suppressor of metastasis were affected by NRF2 stabilization and knockdown. Our result provide comprehensive understanding of NRF2 target genes of drug response, oxidative stress response and metastasis in AsPc-1 metastatic pancreatic cancer cell line.
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Affiliation(s)
- Yong Weon Yi
- Department of Nanobiomedical Science, Graduate School, Dankook University, 119 Dandae-ro, Dongnam-gu, Cheonan-si, Chungnam 330-714 Republic of Korea
| | - Seunghoon Oh
- Department of Physiology, College of Medicine, Dankook University, 119 Dandae-ro, Dongnam-gu, Cheonan-si, Chungnam 330-714 Republic of Korea
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4
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The transcriptional response to oxidative stress during vertebrate development: effects of tert-butylhydroquinone and 2,3,7,8-tetrachlorodibenzo-p-dioxin. PLoS One 2014; 9:e113158. [PMID: 25402455 PMCID: PMC4234671 DOI: 10.1371/journal.pone.0113158] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/20/2014] [Indexed: 01/12/2023] Open
Abstract
Oxidative stress is an important mechanism of chemical toxicity, contributing to teratogenesis and to cardiovascular and neurodegenerative diseases. Developing animals may be especially sensitive to chemicals causing oxidative stress. The developmental expression and inducibility of anti-oxidant defenses through activation of NF-E2-related factor 2 (NRF2) affect susceptibility to oxidants, but the embryonic response to oxidants is not well understood. To assess the response to chemically mediated oxidative stress and how it may vary during development, zebrafish embryos, eleutheroembryos, or larvae at 1, 2, 3, 4, 5, and 6 days post fertilization (dpf) were exposed to DMSO (0.1%), tert-butylhydroquinone (tBHQ; 10 µM) or 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD; 2 nM) for 6 hr. Transcript abundance was assessed by real-time qRT-PCR and microarray. qRT-PCR showed strong (4- to 5-fold) induction of gstp1 by tBHQ as early as 1 dpf. tBHQ also induced gclc (2 dpf), but not sod1, nqo1, or cyp1a. TCDD induced cyp1a but none of the other genes. Microarray analysis showed that 1477 probes were significantly different among the DMSO-, tBHQ-, and TCDD-treated eleutheroembryos at 4 dpf. There was substantial overlap between genes induced in developing zebrafish and a set of marker genes induced by oxidative stress in mammals. Genes induced by tBHQ in 4-dpf zebrafish included those involved in glutathione synthesis and utilization, signal transduction, and DNA damage/stress response. The strong induction of hsp70 determined by microarray was confirmed by qRT-PCR and by use of transgenic zebrafish expressing enhanced green fluorescent protein (EGFP) under control of the hsp70 promoter. Genes strongly down-regulated by tBHQ included mitfa, providing a molecular explanation for the loss of pigmentation in tBHQ-exposed embryos. These data show that zebrafish embryos are responsive to oxidative stress as early as 1 dpf, that responsiveness varies with development in a gene-specific manner, and that the oxidative stress response is substantially conserved in vertebrate animals.
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5
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Singh B, Shoulson R, Chatterjee A, Ronghe A, Bhat NK, Dim DC, Bhat HK. Resveratrol inhibits estrogen-induced breast carcinogenesis through induction of NRF2-mediated protective pathways. Carcinogenesis 2014; 35:1872-80. [PMID: 24894866 DOI: 10.1093/carcin/bgu120] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The importance of estrogens in the etiology of breast cancer is widely recognized. Estrogen-induced oxidative stress has been implicated in this carcinogenic process. Resveratrol (Res), a natural antioxidant phytoestrogen has chemopreventive effects against a variety of illnesses including cancer. The objective of the present study was to characterize the mechanism(s) of Res-mediated protection against estrogen-induced breast carcinogenesis. Female August Copenhagen Irish rats were treated with 17β-estradiol (E2), Res and Res + E2 for 8 months. Cotreatment of rats with Res and E2 inhibited E2-mediated proliferative changes in mammary tissues and significantly increased tumor latency and reduced E2-induced breast tumor development. Resveratrol treatment alone or in combination with E2 significantly upregulated expression of nuclear factor erythroid 2-related factor 2 (NRF2) in mammary tissues. Expression of NRF2-regulated antioxidant genes NQO1, SOD3 and OGG1 that are involved in protection against oxidative DNA damage was increased in Res- and Res + E2-treated mammary tissues. Resveratrol also prevented E2-mediated inhibition of detoxification genes AOX1 and FMO1. Inhibition of E2-mediated alterations in NRF2 promoter methylation and expression of NRF2 targeting miR-93 after Res treatment indicated Res-mediated epigenetic regulation of NRF2 during E2-induced breast carcinogenesis. Resveratrol treatment also induced apoptosis and inhibited E2-mediated increase in DNA damage in mammary tissues. Increased apoptosis and decreased DNA damage, cell migration, colony and mammosphere formation in Res- and Res + E2-treated MCF-10A cells suggested a protective role of Res against E2-induced mammary carcinogenesis. Small-interfering RNA-mediated silencing of NRF2 inhibited Res-mediated preventive effects on the colony and mammosphere formation. Taken together, these results suggest that Res inhibits E2-induced breast carcinogenesis via induction of NRF2-mediated protective pathways.
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Affiliation(s)
- Bhupendra Singh
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA, Institute of Comparative Medicine, Columbia University, New York, NY 10032, USA and Division of Pharmacology and Toxicology, School of Pharmacy and School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Rivka Shoulson
- Institute of Comparative Medicine, Columbia University, New York, NY 10032, USA and
| | | | - Amruta Ronghe
- Division of Pharmacology and Toxicology, School of Pharmacy and
| | - Nimee K Bhat
- Division of Pharmacology and Toxicology, School of Pharmacy and
| | - Daniel C Dim
- School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, USA
| | - Hari K Bhat
- Division of Pharmacology and Toxicology, School of Pharmacy and
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de Miguel FJ, Sharma RD, Pajares MJ, Montuenga LM, Rubio A, Pio R. Identification of alternative splicing events regulated by the oncogenic factor SRSF1 in lung cancer. Cancer Res 2013; 74:1105-15. [PMID: 24371231 DOI: 10.1158/0008-5472.can-13-1481] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abnormal alternative splicing has been associated with cancer. Genome-wide microarrays can be used to detect differential splicing events. In this study, we have developed ExonPointer, an algorithm that uses data from exon and junction probes to identify annotated cassette exons. We used the algorithm to profile differential splicing events in lung adenocarcinoma A549 cells after downregulation of the oncogenic serine/arginine-rich splicing factor 1 (SRSF1). Data were generated using two different microarray platforms. The PCR-based validation rate of the top 20 ranked genes was 60% and 100%. Functional enrichment analyses found a substantial number of splicing events in genes related to RNA metabolism. These analyses also identified genes associated with cancer and developmental and hereditary disorders, as well as biologic processes such as cell division, apoptosis, and proliferation. Most of the top 20 ranked genes were validated in other adenocarcinoma and squamous cell lung cancer cells, with validation rates of 80% to 95% and 70% to 75%, respectively. Moreover, the analysis allowed us to identify four genes, ATP11C, IQCB1, TUBD1, and proline-rich coiled-coil 2C (PRRC2C), with a significantly different pattern of alternative splicing in primary non-small cell lung tumors compared with normal lung tissue. In the case of PRRC2C, SRSF1 downregulation led to the skipping of an exon overexpressed in primary lung tumors. Specific siRNA downregulation of the exon-containing variant significantly reduced cell growth. In conclusion, using a novel analytical tool, we have identified new splicing events regulated by the oncogenic splicing factor SRSF1 in lung cancer.
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Affiliation(s)
- Fernando J de Miguel
- Authors' Affiliations: Division of Oncology, Center for Applied Medical Research (CIMA); Departments of Histology and Pathology and Biochemistry and Genetics, Schools of Science and Medicine, University of Navarra, Pamplona; and CEIT and TECNUN, University of Navarra, San Sebastian, Spain
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von Bernhardi R, Eugenín J. Alzheimer's disease: redox dysregulation as a common denominator for diverse pathogenic mechanisms. Antioxid Redox Signal 2012; 16:974-1031. [PMID: 22122400 DOI: 10.1089/ars.2011.4082] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alzheimer's disease (AD) is the most common cause of dementia and a progressive neurodegeneration that appears to result from multiple pathogenic mechanisms (including protein misfolding/aggregation, involved in both amyloid β-dependent senile plaques and tau-dependent neurofibrillary tangles), metabolic and mitochondrial dysfunction, excitoxicity, calcium handling impairment, glial cell dysfunction, neuroinflammation, and oxidative stress. Oxidative stress, which could be secondary to several of the other pathophysiological mechanisms, appears to be a major determinant of the pathogenesis and progression of AD. The identification of oxidized proteins common for mild cognitive impairment and AD suggests that key oxidation pathways are triggered early and are involved in the initial progression of the neurodegenerative process. Abundant data support that oxidative stress, also considered as a main factor for aging, the major risk factor for AD, can be a common key element capable of articulating the divergent nature of the proposed pathogenic factors. Pathogenic mechanisms influence each other at different levels. Evidence suggests that it will be difficult to define a single-target therapy resulting in the arrest of progression or the improvement of AD deterioration. Since oxidative stress is present from early stages of disease, it appears as one of the main targets to be included in a clinical trial. Exploring the articulation of AD pathogenic mechanisms by oxidative stress will provide clues for better understanding the pathogenesis and progression of this dementing disorder and for the development of effective therapies to treat this disease.
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Affiliation(s)
- Rommy von Bernhardi
- Department of Neurology, Pontificia Universidad Católica de Chile, Santiago, Chile
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8
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Weniger MA, Rizzatti EG, Perez-Galan P, Liu D, Wang Q, Munson PJ, Raghavachari N, White T, Tweito MM, Dunleavy K, Ye Y, Wilson WH, Wiestner A. Treatment-induced oxidative stress and cellular antioxidant capacity determine response to bortezomib in mantle cell lymphoma. Clin Cancer Res 2011; 17:5101-12. [PMID: 21712452 PMCID: PMC3149767 DOI: 10.1158/1078-0432.ccr-10-3367] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
PURPOSE Proteasome inhibition disrupts protein homeostasis and induces apoptosis. Up to 50% of patients with relapsed mantle cell lymphoma (MCL) respond to bortezomib. We used gene expression profiling to investigate the connection between proteasome inhibition, cellular response, and clinical efficacy. EXPERIMENTAL DESIGN We assessed transcriptional changes in primary tumor cells from five patients during treatment with bortezomib in vivo, and in 10 MCL cell lines exposed to bortezomib in vitro, on Affymetrix microarrays. Key findings were confirmed by western blotting. RESULTS MCL cell lines exposed to bortezomib in vitro showed upregulation of endoplasmic reticulum and oxidative stress response pathways. Gene expression changes were strongest in bortezomib-sensitive cells and these cells were also more sensitive to oxidative stress induced by H2O2. Purified tumor cells obtained at several timepoints during bortezomib treatment in 5 previously untreated patients with leukemic MCL showed strong activation of the antioxidant response controlled by NRF2. Unexpectedly, activation of this homeostatic program was significantly stronger in tumors with the best clinical response. Consistent with its proapoptotic function, we found upregulation of NOXA in circulating tumor cells of responding patients. In resistant cells, gene expression changes in response to bortezomib were limited and upregulation of NOXA was absent. Interestingly, at baseline, bortezomib-resistant cells displayed a relatively higher expression of the NRF2 gene-expression signature than sensitive cells (P < 0.001). CONCLUSION Bortezomib triggers an oxidative stress response in vitro and in vivo. High cellular antioxidant capacity contributes to bortezomib resistance.
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Affiliation(s)
- Marc A. Weniger
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health Bethesda, MD
| | - Edgar G. Rizzatti
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health Bethesda, MD
- Fleury Medicina e Saude, Sao Paulo, Brazil
| | - Patricia Perez-Galan
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health Bethesda, MD
| | - Delong Liu
- Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health Bethesda, MD
| | - Qiuyan Wang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Peter J. Munson
- Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health Bethesda, MD
| | - Nalini Raghavachari
- Gene Expression Core Facility, Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health Bethesda, MD
| | - Therese White
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Megan M. Tweito
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Kieron Dunleavy
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yihong Ye
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Wyndham H. Wilson
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Adrian Wiestner
- Hematology Branch, National Heart, Lung and Blood Institute, National Institutes of Health Bethesda, MD
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Player A, Wang Y, Rao M, Kawasaki E. Gene expression analysis of RNA purified from embryonic stem cells and embryoid body-derived cells using a high-throughput microarray platform. CURRENT PROTOCOLS IN STEM CELL BIOLOGY 2008; Chapter 1:Unit 1B.2. [PMID: 18785160 DOI: 10.1002/9780470151808.sc01b02s2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In this unit, starting with purified RNA, experimental protocols for performing microarray expression analysis of embryonic stem cell lines compared to their corresponding differentiated embryocidal bodies are described. Methods for data analysis are suggested, with the goal of determining which genes are differentially expressed between the preparations. As an example, the use of the Affymetrix microarray expression platform is described, but alternative experimental options for analysis of RNA transcript levels are also summarized. This unit suggests quality control metrics, summarizes the critical parameters necessary for obtaining reproducible experimental results, and outlines quantitative PCR methods for validating microarray results.
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10
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Brouard S, Mansfield E, Braud C, Li L, Giral M, Hsieh SC, Baeten D, Zhang M, Ashton-Chess J, Braudeau C, Hsieh F, Dupont A, Pallier A, Moreau A, Louis S, Ruiz C, Salvatierra O, Soulillou JP, Sarwal M. Identification of a peripheral blood transcriptional biomarker panel associated with operational renal allograft tolerance. Proc Natl Acad Sci U S A 2007; 104:15448-53. [PMID: 17873064 PMCID: PMC2000539 DOI: 10.1073/pnas.0705834104] [Citation(s) in RCA: 283] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Indexed: 12/13/2022] Open
Abstract
Long-term allograft survival generally requires lifelong immunosuppression (IS). Rarely, recipients display spontaneous "operational tolerance" with stable graft function in the absence of IS. The lack of biological markers of this phenomenon precludes identification of potentially tolerant patients in which IS could be tapered and hinders the development of new tolerance-inducing strategies. The objective of this study was to identify minimally invasive blood biomarkers for operational tolerance and use these biomarkers to determine the frequency of this state in immunosuppressed patients with stable graft function. Blood gene expression profiles from 75 renal-transplant patient cohorts (operational tolerance/acute and chronic rejection/stable graft function on IS) and 16 healthy individuals were analyzed. A subset of samples was used for microarray analysis where three-class comparison of the different groups of patients identified a "tolerant footprint" of 49 genes. These biomarkers were applied for prediction of operational tolerance by microarray and real-time PCR in independent test groups. Thirty-three of 49 genes correctly segregated tolerance and chronic rejection phenotypes with 99% and 86% specificity. The signature is shared with 1 of 12 and 5 of 10 stable patients on triple IS and low-dose steroid monotherapy, respectively. The gene signature suggests a pattern of reduced costimulatory signaling, immune quiescence, apoptosis, and memory T cell responses. This study identifies in the blood of kidney recipients a set of genes associated with operational tolerance that may have utility as a minimally invasive monitoring tool for guiding IS titration. Further validation of this tool for safe IS minimization in prospective clinical trials is warranted.
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Affiliation(s)
- Sophie Brouard
- Institut National de la Santé et de la Recherche Médicale, U643, Centre Hospitalier Universitaire de Nantes, Institut de Transplantation et de Recherche en Transplantation, and Université de Nantes, Faculte de Medicine, F-44000 Nantes, France
| | - Elaine Mansfield
- Department of Pediatrics, Stanford University, 300 Pasteur Drive, Stanford, CA 94304
- Affymetrix, Inc., 3380 Central Expressway, Santa Clara, CA 95051
| | - Christophe Braud
- Institut National de la Santé et de la Recherche Médicale, U643, Centre Hospitalier Universitaire de Nantes, Institut de Transplantation et de Recherche en Transplantation, and Université de Nantes, Faculte de Medicine, F-44000 Nantes, France
| | - Li Li
- Department of Pediatrics, Stanford University, 300 Pasteur Drive, Stanford, CA 94304
| | - Magali Giral
- Institut National de la Santé et de la Recherche Médicale, U643, Centre Hospitalier Universitaire de Nantes, Institut de Transplantation et de Recherche en Transplantation, and Université de Nantes, Faculte de Medicine, F-44000 Nantes, France
| | - Szu-chuan Hsieh
- Department of Pediatrics, Stanford University, 300 Pasteur Drive, Stanford, CA 94304
| | - Dominique Baeten
- Institut National de la Santé et de la Recherche Médicale, U643, Centre Hospitalier Universitaire de Nantes, Institut de Transplantation et de Recherche en Transplantation, and Université de Nantes, Faculte de Medicine, F-44000 Nantes, France
- Clinical Immunology and Rheumatology, Academic Medical Center/University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands; and
| | - Meixia Zhang
- Department of Pediatrics, Stanford University, 300 Pasteur Drive, Stanford, CA 94304
- Department of Clinical Pharmacology, China Medical University, Shenyang 110001, China
| | - Joanna Ashton-Chess
- Institut National de la Santé et de la Recherche Médicale, U643, Centre Hospitalier Universitaire de Nantes, Institut de Transplantation et de Recherche en Transplantation, and Université de Nantes, Faculte de Medicine, F-44000 Nantes, France
| | - Cécile Braudeau
- Institut National de la Santé et de la Recherche Médicale, U643, Centre Hospitalier Universitaire de Nantes, Institut de Transplantation et de Recherche en Transplantation, and Université de Nantes, Faculte de Medicine, F-44000 Nantes, France
| | - Frank Hsieh
- Department of Veterans Affairs Palo Alto Health Care System (151-K), Palo Alto, CA 94304
| | - Alexandre Dupont
- Institut National de la Santé et de la Recherche Médicale, U643, Centre Hospitalier Universitaire de Nantes, Institut de Transplantation et de Recherche en Transplantation, and Université de Nantes, Faculte de Medicine, F-44000 Nantes, France
| | - Annaik Pallier
- Institut National de la Santé et de la Recherche Médicale, U643, Centre Hospitalier Universitaire de Nantes, Institut de Transplantation et de Recherche en Transplantation, and Université de Nantes, Faculte de Medicine, F-44000 Nantes, France
| | - Anne Moreau
- Service d'Anatomie Pathologique, CHU Hôtel-Dieu, 30 Bd Jean Monnet, 44093 Nantes Cedex 01, France
| | - Stéphanie Louis
- Institut National de la Santé et de la Recherche Médicale, U643, Centre Hospitalier Universitaire de Nantes, Institut de Transplantation et de Recherche en Transplantation, and Université de Nantes, Faculte de Medicine, F-44000 Nantes, France
| | - Catherine Ruiz
- TcLand, Halle 13 Bio-Ouest Ile de Nantes, 21 Rue de la Noue Bras de Fer, 44200 Nantes, France
| | - Oscar Salvatierra
- Department of Pediatrics, Stanford University, 300 Pasteur Drive, Stanford, CA 94304
| | - Jean-Paul Soulillou
- Institut National de la Santé et de la Recherche Médicale, U643, Centre Hospitalier Universitaire de Nantes, Institut de Transplantation et de Recherche en Transplantation, and Université de Nantes, Faculte de Medicine, F-44000 Nantes, France
| | - Minnie Sarwal
- Department of Pediatrics, Stanford University, 300 Pasteur Drive, Stanford, CA 94304
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Stafford P, Brun M. Three methods for optimization of cross-laboratory and cross-platform microarray expression data. Nucleic Acids Res 2007; 35:e72. [PMID: 17478523 PMCID: PMC1904274 DOI: 10.1093/nar/gkl1133] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Microarray gene expression data becomes more valuable as our confidence in the results grows. Guaranteeing data quality becomes increasingly important as microarrays are being used to diagnose and treat patients (1–4). The MAQC Quality Control Consortium, the FDA's Critical Path Initiative, NCI's caBIG and others are implementing procedures that will broadly enhance data quality. As GEO continues to grow, its usefulness is constrained by the level of correlation across experiments and general applicability. Although RNA preparation and array platform play important roles in data accuracy, pre-processing is a user-selected factor that has an enormous effect. Normalization of expression data is necessary, but the methods have specific and pronounced effects on precision, accuracy and historical correlation. As a case study, we present a microarray calibration process using normalization as the adjustable parameter. We examine the impact of eight normalizations across both Agilent and Affymetrix expression platforms on three expression readouts: (1) sensitivity and power, (2) functional/biological interpretation and (3) feature selection and classification error. The reader is encouraged to measure their own discordant data, whether cross-laboratory, cross-platform or across any other variance source, and to use their results to tune the adjustable parameters of their laboratory to ensure increased correlation.
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Affiliation(s)
- Phillip Stafford
- Biodesign Institute, Arizona State University, Center for Innovations in Medicine, Tempe, AZ, USA
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Nguyen ST, Hasegawa S, Tsuda H, Tomioka H, Ushijima M, Noda M, Omura K, Miki Y. Identification of a predictive gene expression signature of cervical lymph node metastasis in oral squamous cell carcinoma. Cancer Sci 2007; 98:740-6. [PMID: 17391312 PMCID: PMC11158652 DOI: 10.1111/j.1349-7006.2007.00454.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
An accurate assessment of the cervical lymph node metastasis status in oral cavity cancer not only helps predict the prognosis of patients, but also helps surgeons to perform the appropriate treatment. We investigated the utilization of microarray technology focusing on the differences in gene expression profiles between primary tumors of oral squamous cell carcinoma that had metastasized to cervical lymph nodes and those that had not metastasized in the hope of finding new biomarkers to serve for diagnosis and treatment of oral cavity cancer. To design this experiment, we prepared two groups: the learning case group with 30 patients and the test case group with 13 patients. All tissue samples were performed using laser captured microdissection to yield cancer cells, and RNA was isolated from purified cancer cells. To identify a predictive gene expression signature, the different gene expressions between the two groups with and without metastasis in the learning case (n = 30) were analyzed, and the 85 genes expressed differentially were selected. Subsequently, to construct a more accurate prediction model, we further selected the genes with a high power for prediction from the 85 genes using the AdaBoost algorithm. The eight candidate genes, DCTD, IL-15, THBD, GSDML, SH3GL3, PTHLH, RP5-1022P6 and C9orf46, were selected to achieve the minimum error rate. Quantitative reverse transcription-polymerase chain reaction was carried out to validate the selected genes. From these statistical methods, the prediction model was constructed including the eight genes and this model was evaluated by using the test case group. The results in 12 of 13 cases ( approximately 92.3%) were predicted correctly.
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Affiliation(s)
- Su Tien Nguyen
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
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Barnes M, Freudenberg J, Thompson S, Aronow B, Pavlidis P. Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res 2005; 33:5914-23. [PMID: 16237126 PMCID: PMC1258170 DOI: 10.1093/nar/gki890] [Citation(s) in RCA: 190] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The growth in popularity of RNA expression microarrays has been accompanied by concerns about the reliability of the data especially when comparing between different platforms. Here, we present an evaluation of the reproducibility of microarray results using two platforms, Affymetrix GeneChips and Illumina BeadArrays. The study design is based on a dilution series of two human tissues (blood and placenta), tested in duplicate on each platform. The results of a comparison between the platforms indicate very high agreement, particularly for genes which are predicted to be differentially expressed between the two tissues. Agreement was strongly correlated with the level of expression of a gene. Concordance was also improved when probes on the two platforms could be identified as being likely to target the same set of transcripts of a given gene. These results shed light on the causes or failures of agreement across microarray platforms. The set of probes we found to be most highly reproducible can be used by others to help increase confidence in analyses of other data sets using these platforms.
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Affiliation(s)
| | - Johannes Freudenberg
- Cincinnati Children's Hospital Medical Center, Division of Biomedical InformaticsCincinnati OH, USA
| | | | - Bruce Aronow
- Cincinnati Children's Hospital Medical Center, Division of Biomedical InformaticsCincinnati OH, USA
| | - Paul Pavlidis
- Columbia University Department of Biomedical InformaticsNew York, NY, USA
- To whom correspondence should be addressed. Tel: +1 212 851 5141; Fax: +1 212 851 5290;
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Ahmed SH, Lutjens R, van der Stap LD, Lekic D, Romano-Spica V, Morales M, Koob GF, Repunte-Canonigo V, Sanna PP. Gene expression evidence for remodeling of lateral hypothalamic circuitry in cocaine addiction. Proc Natl Acad Sci U S A 2005; 102:11533-8. [PMID: 16076954 PMCID: PMC1183574 DOI: 10.1073/pnas.0504438102] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Indexed: 11/18/2022] Open
Abstract
By using high-density oligonucleotide arrays, we profiled gene expression in reward-related brain regions of rats that developed escalated cocaine intake after extended access to cocaine (6 h per day). Rats allowed restricted daily access to cocaine (only 1 h) that displayed a stable level of cocaine intake and cocaine naive rats were used for controls. Four analysis methods were compared: Affymetrix microarray suite 4 and microarray suite 5, which use perfect-match-minus-mismatch models, and dchip and rma, which use perfect-match-only models to generate expression values. Results were validated by RT-PCR in individual animals from an independent replication of the experiment. A small number of genes was associated with escalated cocaine intake (ESC genes). Unexpectedly, of the brain regions examined [prefrontal cortex, nucleus accumbens, septum, lateral hypothalamus (LH), amygdala, and ventral tegmental area], the LH was the most transcriptionally responsive in escalation of cocaine intake. Most of the ESC genes identified are also expressed during synaptogenesis and synaptic plasticity and include genes that code for several presynaptic and postsynaptic proteins involved in neurotransmission. These results suggest that LH intrinsic circuitry undergoes a structural reorganization during escalation of cocaine use. This remodeling of LH circuitry could contribute to the chronic deficit in reward function that has been hypothesized to drive the transition to drug addiction. Results also support the value of using multiple analysis strategies to identify the most robust changes in gene expression and to compensate for the biases that affect each strategy.
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Affiliation(s)
- Serge H Ahmed
- Department of Neuropharmacology, The Scripps Research Institute, La Jolla, CA 92103, USA
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