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Ta R, Santini C, Gou P, Lee G, Tai YC, O'Brien C, Fontecha M, Grant C, Bacon L, Finn S, Vandenberghe E, Quinn F, Dua R, Flavin R. Molecular Subtyping of Diffuse Large B-Cell Lymphoma Using a Novel Quantitative RT-PCR Assay. J Mol Diagn 2020; 23:323-340. [PMID: 33385586 DOI: 10.1016/j.jmoldx.2020.11.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/20/2020] [Accepted: 11/25/2020] [Indexed: 11/25/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease. Cell-of-origin classification in DLBCL has identified activated B cell (ABC) and germinal center B cell (GCB) as two major subtypes. Patients with the ABC subtype show reduced overall survival with standard therapies. Development of a quantitative RT-PCR-based lymphoma cell-of-origin (LCOO) assay to determine ABC, GCB, and unclassifiable subtypes in formalin-fixed, paraffin-embedded tissue (FFPET) DLBCL samples is reported. The LCOO classifier was trained on two DLBCL cohorts with validation performed by using an analytical grade assay in an independent cohort of 60 FFPET DLBCL samples. In the validation cohort, LCOO classification was 88.1%, 84.7%, and 84.7% concordant with microarray, immunohistochemistry (Hans classification), and Lymphoma Subtyping Test, respectively. Importantly, LCOO and Lymphoma Subtyping Test assays commonly assigned subtypes in 17 (94.4%) of 18 ABC samples and 34 (89.5%) of 38 GCB DLBCL samples from this cohort. Progression-free survival and overall survival of ABC and GCB subtypes, as classified by all platforms, were not significantly different in the validation cohort. LCOO classification using publicly available microarray gene expression from two independent data sets (414 fresh frozen and 474 FFPET DLBCL biopsies) revealed a significantly worse outcome for the ABC subtype compared with that of the GCB subtype. Thus, a sensitive, reproducible, LCOO assay developed on an easy to standardize quantitative RT-PCR platform may be an important clinical tool for DLBCL cell-of-origin classification.
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Affiliation(s)
- Robert Ta
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts; Department of Cancer Molecular Diagnostics, St. James's Hospital, Dublin, Ireland; Department of Histopathology, St. James's Hospital, Dublin, Ireland
| | - Chris Santini
- Department of PCR IVD Research and Early Development, Roche Molecular Systems, Inc., Pleasanton, California
| | - Patricia Gou
- Department of Histopathology, St. James's Hospital, Dublin, Ireland
| | - Greg Lee
- Department of Haematology, St. James's Hospital, Dublin, Ireland
| | - Yu Chuan Tai
- Department of Bioinformatics, Roche Molecular Systems, Inc., Pleasanton, California
| | - Cathal O'Brien
- Department of Cancer Molecular Diagnostics, St. James's Hospital, Dublin, Ireland; Trinity College, Dublin, Ireland
| | - Marcel Fontecha
- Department of PCR IVD Research and Early Development, Roche Molecular Systems, Inc., Pleasanton, California
| | - Cliona Grant
- Department of Oncology, St. James's Hospital, Dublin, Ireland
| | - Larry Bacon
- Department of Haematology, St. James's Hospital, Dublin, Ireland; Trinity College, Dublin, Ireland
| | - Stephen Finn
- Department of Cancer Molecular Diagnostics, St. James's Hospital, Dublin, Ireland; Department of Histopathology, St. James's Hospital, Dublin, Ireland; Trinity College, Dublin, Ireland
| | - Elisabeth Vandenberghe
- Department of Cancer Molecular Diagnostics, St. James's Hospital, Dublin, Ireland; Department of Haematology, St. James's Hospital, Dublin, Ireland; Trinity College, Dublin, Ireland
| | - Fiona Quinn
- Department of Cancer Molecular Diagnostics, St. James's Hospital, Dublin, Ireland; Trinity College, Dublin, Ireland
| | - Rajiv Dua
- Department of PCR IVD Research and Early Development, Roche Molecular Systems, Inc., Pleasanton, California.
| | - Richard Flavin
- Department of Cancer Molecular Diagnostics, St. James's Hospital, Dublin, Ireland; Department of Histopathology, St. James's Hospital, Dublin, Ireland; Trinity College, Dublin, Ireland
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2
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Hu-Lieskovan S, Bhaumik S, Dhodapkar K, Grivel JCJB, Gupta S, Hanks BA, Janetzki S, Kleen TO, Koguchi Y, Lund AW, Maccalli C, Mahnke YD, Novosiadly RD, Selvan SR, Sims T, Zhao Y, Maecker HT. SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery. J Immunother Cancer 2020; 8:e000705. [PMID: 33268350 PMCID: PMC7713206 DOI: 10.1136/jitc-2020-000705] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2020] [Indexed: 02/07/2023] Open
Abstract
Since the publication of the Society for Immunotherapy of Cancer's (SITC) original cancer immunotherapy biomarkers resource document, there have been remarkable breakthroughs in cancer immunotherapy, in particular the development and approval of immune checkpoint inhibitors, engineered cellular therapies, and tumor vaccines to unleash antitumor immune activity. The most notable feature of these breakthroughs is the achievement of durable clinical responses in some patients, enabling long-term survival. These durable responses have been noted in tumor types that were not previously considered immunotherapy-sensitive, suggesting that all patients with cancer may have the potential to benefit from immunotherapy. However, a persistent challenge in the field is the fact that only a minority of patients respond to immunotherapy, especially those therapies that rely on endogenous immune activation such as checkpoint inhibitors and vaccination due to the complex and heterogeneous immune escape mechanisms which can develop in each patient. Therefore, the development of robust biomarkers for each immunotherapy strategy, enabling rational patient selection and the design of precise combination therapies, is key for the continued success and improvement of immunotherapy. In this document, we summarize and update established biomarkers, guidelines, and regulatory considerations for clinical immune biomarker development, discuss well-known and novel technologies for biomarker discovery and validation, and provide tools and resources that can be used by the biomarker research community to facilitate the continued development of immuno-oncology and aid in the goal of durable responses in all patients.
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Affiliation(s)
- Siwen Hu-Lieskovan
- Huntsman Cancer Institute, Salt Lake City, UT, USA
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Kavita Dhodapkar
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | | | - Sumati Gupta
- Huntsman Cancer Institute, Salt Lake City, Utah, USA
| | - Brent A Hanks
- Duke University Medical Center, Durham, North Carolina, USA
| | | | | | - Yoshinobu Koguchi
- Earle A Chiles Research Institute, Providence Cancer Institute, Portland, Oregon, USA
| | - Amanda W Lund
- Oregon Health and Science University, Portland, Oregon, USA
| | | | | | | | | | - Tasha Sims
- Regeneron Pharmaceuticals Inc, Tarrytown, New York, USA
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3
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Sadowski SM, Petrenko V, Meyer P, Pusztaszeri M, Brulhart-Meynet MC, Heddad Masson M, Triponez F, Philippe J, Dibner C. Validation of molecular biomarkers for preoperative diagnostics of human papillary thyroid carcinoma in fine needle aspirates. Gland Surg 2019; 8:S62-S76. [PMID: 31475093 DOI: 10.21037/gs.2018.11.04] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Background Despite substantial efforts, reliable preoperative diagnostic for human thyroid malignancies in case of cytologically indeterminate nodules is still missing, resulting in high number of unnecessary thyroidectomies. In an attempt to increase precision of existing preoperative diagnostics, we aimed at validating the panel of molecular biomarkers predictive for papillary thyroid carcinoma (PTC) in preoperative fine needle aspirate (FNA) samples. Methods In this prospective study conducted in preoperative thyroid FNA from 44 thyroid nodules, expression levels of 11 molecular biomarkers previously validated on the postoperative samples of PTCs were measured by Cell-to-CT and QuantiGene Plex methods and correlated with final diagnosis. Results The QuantiGene Plex resulted in reliable gene expression measurements for FNA and core-needle biopsy (CNB) samples, however this method was less sensitive than pre-amplification based Cell-to-CT. Measurements conducted on the same samples by the two methods significantly correlated for most of the genes. Expression levels of TIMP1, c-MET and ARNTL were upregulated in PTC nodules as compared to benign counterparts, supporting previous post-operative studies. Strong correlation was observed between these biomarker alterations in the same samples. Within the sub-group of 15 indeterminate nodules (Bethesda II-V), TIMP1 had 100% specificity and 83% sensitivity for PTC cases. Conclusions Assessment of TIMP1, c-MET and core-clock gene ARNTL expression levels by QuantiGene Plex assay in FNA samples holds promise as an ancillary method to the cytological preoperative diagnostics.
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Affiliation(s)
- Samira M Sadowski
- Department of Thoracic and Endocrine Surgery, University Hospital of Geneva and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Volodymyr Petrenko
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, Geneva, Switzerland.,Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Diabetes Centre, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,iGE3 Center, Geneva, Switzerland
| | - Patrick Meyer
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, Geneva, Switzerland
| | - Marc Pusztaszeri
- Department of Pathology, Jewish General Hospital and McGill University, Montreal, Canada
| | - Marie-Claude Brulhart-Meynet
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, Geneva, Switzerland.,Diabetes Centre, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Mounia Heddad Masson
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, Geneva, Switzerland.,Diabetes Centre, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Frédéric Triponez
- Department of Thoracic and Endocrine Surgery, University Hospital of Geneva and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Jacques Philippe
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, Geneva, Switzerland.,Diabetes Centre, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Charna Dibner
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, Geneva, Switzerland.,Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Diabetes Centre, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,iGE3 Center, Geneva, Switzerland
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4
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Verbist B, Adriaensen E, Keersmaekers V, Putri D, Crabbe M, Derks M, Bagdziunas R, Laenen G, De Wolf H. Analyzing magnetic bead QuantiGene® Plex 2.0 gene expression data in high throughput mode using QGprofiler. BMC Bioinformatics 2019; 20:378. [PMID: 31286864 PMCID: PMC6615108 DOI: 10.1186/s12859-019-2975-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/28/2019] [Indexed: 12/23/2022] Open
Abstract
Background The QuantiGene® Plex 2.0 platform (ThermoFisher Scientific) combines bDNA with the Luminex/xMAP magnetic bead capturing technology to assess differential gene expression in a compound exposure setting. This technology allows multiplexing in a single well of a 96 or 384 multi-well plate and can thus be used in high throughput drug discovery mode. Data interpretation follows a three-step normalization/transformation flow in which raw median fluorescent gene signals are transformed to fold change values with the use of proper housekeeping genes and negative controls. Clear instructions on how to assess the data quality and tools to perform this analysis in high throughput mode are, however, currently lacking. Results In this paper we introduce QGprofiler, an open source R based shiny application. QGprofiler allows for proper QuantiGene® Plex 2.0 assay optimization, choice of housekeeping genes and data pre-processing up to fold change, including appropriate QC metrics. In addition, QGprofiler allows for an Akaike information criterion based dose response fold change model selection and has a built-in tool to detect the cytotoxic potential of compounds evaluated in a high throughput screening campaign. Conclusion QGprofiler is a user friendly, open source available R based shiny application, which is developed to support drug discovery campaigns. In this context, entire compound libraries/series can be tested in dose response against a gene signature of choice in search for new disease relevant chemical entities. QGprofiler is available at: https://qgprofiler.openanalytics.eu/app/QGprofiler Electronic supplementary material The online version of this article (10.1186/s12859-019-2975-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bie Verbist
- Janssen R&D, TMEDS, Turnhoutseweg 30, 2340, Beerse, BE, Belgium
| | - Eva Adriaensen
- Karel de Grote Hogeschool, Groenplaats, 2020, Antwerpen, BE, Belgium
| | - Vikki Keersmaekers
- Janssen R&D, Discovery Biology, Oncology Heme, Turnhoutseweg 30, 2340, Beerse, BE, Belgium
| | - Dea Putri
- Janssen R&D, TMEDS, Turnhoutseweg 30, 2340, Beerse, BE, Belgium
| | | | - Maarten Derks
- Janssen R&D, Discovery Biology, Oncology Heme, Turnhoutseweg 30, 2340, Beerse, BE, Belgium
| | | | - Griet Laenen
- Open Analytics, Jupiterstraat 20, 2600, Antwerpen, BE, Belgium
| | - Hans De Wolf
- Janssen R&D, DS, Turnhoutseweg 30, 2340, Beerse, BE, Belgium.
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5
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Scerri J, Baldacchino S, Saliba C, Scerri C, Grech G. Bead-based RNA multiplex panels for biomarker detection in oncology samples. Methods 2019; 158:86-91. [PMID: 30352255 DOI: 10.1016/j.ymeth.2018.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 09/29/2018] [Accepted: 10/16/2018] [Indexed: 12/17/2022] Open
Abstract
Patient stratification, prognosis and disease monitoring are three important aspects of personalized cancer medicine. With traditional serum tumour protein biomarkers showing lack of specificity and sensitivity, and tumour heterogeneity affecting the response to targeted therapy based on tissue biomarkers, the focus has shifted to the use of molecular tumour signatures as specific biomarkers. Multiplex microsphere-based panels are robust and cost-effective, high throughput molecular assays, which can accurately characterize tumours even from small amounts of poor quality nucleic acids. Only few studies have reported the use of microspheres (beads) to quantify RNA expression of targets of interest simultaneously (multiplexing). This review is an overview of the various applications of bead-based RNA panels in molecular oncology, with focus on the Invitrogen™ QuantiGene™ Plex Assay (Thermo Fisher Scientific), and provides a comparison with PCR-based and other methodologies. The advantages of multiplex bead assays are exemplified by the quantification of RNA expression in formalin-fixed, paraffin embedded (FFPE) archival tissue and the simultaneous detection of biomarkers in low input samples, including quantification of markers in microdissected tissue material, to characterise heterogeneous tumour sites within a sample, and by the detection of markers in low numbers of circulating tumour cells.
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Affiliation(s)
- Jeanesse Scerri
- Department of Physiology & Biochemistry, Faculty of Medicine and Surgery, University of Malta, Malta.
| | - Shawn Baldacchino
- Department of Pathology, Faculty of Medicine & Surgery, University of Malta, Malta.
| | - Christian Saliba
- Centre for Molecular Medicine and Biobanking, University of Malta, Malta.
| | - Christian Scerri
- Department of Physiology & Biochemistry, Faculty of Medicine and Surgery, University of Malta, Malta.
| | - Godfrey Grech
- Department of Pathology, Faculty of Medicine & Surgery, University of Malta, Malta.
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6
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Mohd Mutalip SS, Rajikin MH, Ab Rahim S, Mohamed Noor Khan N. Annatto ( Bixa orellana) δ-TCT Supplementation Protection against Embryonic Malformations through Alterations in PI3K/Akt-Cyclin D1 Pathway. Biomolecules 2019; 9:E19. [PMID: 30634632 PMCID: PMC6358786 DOI: 10.3390/biom9010019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 12/12/2022] Open
Abstract
Protective action by annatto-derived delta-tocotrienol (δ-TCT) and soy-derived alpha-tocopherol (α-TOC) through the regulation of the PI3K/Akt-cyclin D1 pathway against nicotine-induced DNA damage is the focus of the present study. Nicotine, which has been widely reported to have numerous adverse effects on the reproductive system, was used as a reproductive toxicant. 48 female balb/c mice (6⁻8 weeks) (23⁻25 g) were randomly divided into eight groups (Grp.1⁻Grp.8; n = 6) and treated with either nicotine or/and annatto δ-TCT/soy α-TOC for seven consecutive days. On Day 8, the females were superovulated and mated before euthanization for embryo collection (46 h post-coitum). Fifty 2-cell embryos from each group were used in gene expression analysis using Affymetrix QuantiGene Plex2.0 assay. Findings indicated that nicotine (Grp.2) significantly decreased (p < 0.05) the number of produced 2-cell embryos compared to the control (Grp.1). Intervention with mixed annatto δ-TCT (Grp.3) and pure annatto δ-TCT (Grp.4) significantly increased the number of produced 2-cell embryos by 127% and 79%, respectively compared to Grp.2, but these were lower than Grp.1. Concurrent treatment with soy α-TOC (Grp.5) decreased embryo production by 7%. Supplementations with δ-TCT and α-TOC alone (Grp.6-Grp.8) significantly increased (p < 0.05) the number of produced 2-cell embryos by 50%, 36%, and 41%, respectively, compared to control (Grp.1). These results were found to be associated with alterations in the PI3K/Akt-Cyclin D1 genes expressions, indicating the inhibitory effects of annatto δ-TCT and soy α-TOC against nicotinic embryonic damage. To our knowledge, this is the first attempt in studying the benefits of annatto δ-TCT on murine preimplantation 2-cell embryos.
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Affiliation(s)
- Siti Syairah Mohd Mutalip
- Faculty of Pharmacy, Universiti Teknologi MARA (UiTM) Puncak Alam Campus, Selangor 42300, Malaysia.
- Maternofetal and Embryo Research Group (MatE), Universiti Teknologi MARA (UiTM), Selangor 40450, Malaysia.
| | - Mohd Hamim Rajikin
- Maternofetal and Embryo Research Group (MatE), Universiti Teknologi MARA (UiTM), Selangor 40450, Malaysia.
- Faculty of Medicine, Universiti Teknologi MARA (UiTM) Sg. Buloh Campus, Selangor 47000, Malaysia.
| | - Sharaniza Ab Rahim
- Faculty of Medicine, Universiti Teknologi MARA (UiTM) Sg. Buloh Campus, Selangor 47000, Malaysia.
| | - Norashikin Mohamed Noor Khan
- Maternofetal and Embryo Research Group (MatE), Universiti Teknologi MARA (UiTM), Selangor 40450, Malaysia.
- Faculty of Medicine, Universiti Teknologi MARA (UiTM) Sg. Buloh Campus, Selangor 47000, Malaysia.
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7
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Chen W, Wang P. Molecular Analysis for Characterizing Transgenic Events. Methods Mol Biol 2019; 1864:397-410. [PMID: 30415348 DOI: 10.1007/978-1-4939-8778-8_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To develop a commercial trait product, a large number of transgenic events are often produced to obtain the event with desired level of expression. It is crucial to develop efficient and sensitive molecular characterization methods to advance events with stable transgene expression, free of vector backbone sequences and without major changes to the native genome caused by transgene insertion. Here, we discuss a variety of analytical tools, including quantitative PCR (qPCR), Southern blot analysis, and various sequencing technologies, which have been widely used to determine the insert copy number, presence/absence of vector backbone sequences, integrity of the T-DNA, and genomic location of the T-DNA insertion. Moreover, since the discovery of RNA interference in 1998 (Fire et al., Nature 391:806-811, 1998), RNAi has emerged as another powerful tool in in the development of a new transgenic trait for insect control. RNAi creates a double-stranded RNA duplex as the active molecule which forms a strong secondary structure, resulting in challenges for detection. In addition to molecular analysis at the DNA level, this chapter describes detection methods of the active molecules (i.e., double-stranded RNA) for RNAi-based traits.
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MESH Headings
- Biotechnology/instrumentation
- Biotechnology/methods
- Blotting, Southern
- Commerce
- Crops, Agricultural/genetics
- DNA, Bacterial/genetics
- DNA, Plant/analysis
- DNA, Plant/genetics
- Genome, Plant/genetics
- Plants, Genetically Modified/genetics
- Polymerase Chain Reaction
- Quantitative Trait Loci/genetics
- RNA Interference
- RNA, Double-Stranded/analysis
- RNA, Double-Stranded/genetics
- RNA, Plant/analysis
- RNA, Plant/genetics
- Transformation, Genetic
- Transgenes/genetics
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Affiliation(s)
- Wei Chen
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA.
| | - PoHao Wang
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, USA
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8
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Mills MG, Gallagher EP. A targeted gene expression platform allows for rapid analysis of chemical-induced antioxidant mRNA expression in zebrafish larvae. PLoS One 2017; 12:e0171025. [PMID: 28212397 PMCID: PMC5315391 DOI: 10.1371/journal.pone.0171025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 01/13/2017] [Indexed: 12/11/2022] Open
Abstract
Chemical-induced oxidative stress and the biochemical pathways that protect against oxidative damage are of particular interest in the field of toxicology. To rapidly identify oxidative stress-responsive gene expression changes in zebrafish, we developed a targeted panel of antioxidant genes using the Affymetrix QuantiGene Plex (QGP) platform. The genes contained in our panel include eight putative Nrf2 (Nfe2l2a)-dependent antioxidant genes (hmox1a, gstp1, gclc, nqo1, prdx1, gpx1a, sod1, sod2), a stress response gene (hsp70), an inducible DNA damage repair gene (gadd45bb), and three reference genes (actb1, gapdh, hprt1). We tested this platform on larval zebrafish exposed to tert-butyl hydroperoxide (tBHP) and cadmium (Cd), two model oxidative stressors with different modes of action, and compared our results with those obtained using the more common quantitative PCR (qPCR) method. Both methods showed that exposure to tBHP and Cd induced expression of prdx1, gstp1, and hmox1a (2- to 12-fold increase via QGP), indicative of an activated Nrf2 response in larval zebrafish. Both compounds also elicited a general stress response as reflected by elevation of hsp70 and gadd45bb, with Cd being the more potent inducer. Transient changes were observed in sod2 and gpx1a expression, whereas nqo1, an Nrf2-responsive gene in mammalian cells, was minimally affected by either tBHP or Cd chemical exposures. Developmental expression analysis of the target genes by QGP revealed marked upregulation of sod2 between 0-96hpf, and to a lesser extent, of sod1 and gstp1. Once optimized, QGP analysis of these experiments was accomplished more rapidly, using far less tissue, and at lower total costs than qPCR analysis. In summary, the QGP platform as applied to higher-throughput zebrafish studies provides a reasonable cost-effective alternative to qPCR or more comprehensive transcriptomics approaches to rapidly assess the potential for chemicals to elicit oxidative stress as a mechanism of chemical toxicity.
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Affiliation(s)
- Margaret G. Mills
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Evan P. Gallagher
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States of America
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9
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Araf S, Korfi K, Rahim T, Davies A, Fitzgibbon J. Advances in the molecular diagnosis of diffuse large B-cell lymphoma in the era of precision medicine. Expert Rev Mol Diagn 2016; 16:1093-1102. [PMID: 27648481 DOI: 10.1080/14737159.2016.1235974] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION The adoption of high-throughput technologies has led to a transformation in our ability to classify diffuse large B-cell lymphoma (DLBCL) into unique molecular subtypes. In parallel, the expansion of agents targeting key genetic and gene expression signatures has led to an unprecedented opportunity to personalize cancer therapies, paving the way for precision medicine. Areas covered: This review summarizes the key molecular subtypes of DLBCL and outlines the novel technology platforms in development to discriminate clinically relevant subtypes. Expert commentary: The application of emerging diagnostic tests into routine clinical practise is gaining momentum following the demonstration of subtype specific activity by novel agents. Co-ordinated efforts are required to ensure that these state of the art technologies provide reliable and clinically meaningful results accessible to the wider haematology community.
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MESH Headings
- Biomarkers, Tumor
- Gene Expression
- Genes, bcl-2
- Genes, myc
- High-Throughput Nucleotide Sequencing
- Humans
- Lymphoma, Large B-Cell, Diffuse/diagnosis
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/mortality
- Lymphoma, Large B-Cell, Diffuse/therapy
- Molecular Diagnostic Techniques
- Mutation
- Precision Medicine/methods
- Prognosis
- Transcriptome
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Affiliation(s)
- Shamzah Araf
- a Centre for Haemato-Oncology , Barts Cancer Institute, Queen Mary University of London , London , UK
| | - Koorosh Korfi
- a Centre for Haemato-Oncology , Barts Cancer Institute, Queen Mary University of London , London , UK
| | - Tahrima Rahim
- a Centre for Haemato-Oncology , Barts Cancer Institute, Queen Mary University of London , London , UK
| | - Andrew Davies
- b Cancer Sciences Unit, Faculty of Medicine , University of Southampton , Southampton , UK
| | - Jude Fitzgibbon
- a Centre for Haemato-Oncology , Barts Cancer Institute, Queen Mary University of London , London , UK
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10
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Coles AH, Osborn MF, Alterman JF, Turanov AA, Godinho BMDC, Kennington L, Chase K, Aronin N, Khvorova A. A High-Throughput Method for Direct Detection of Therapeutic Oligonucleotide-Induced Gene Silencing In Vivo. Nucleic Acid Ther 2015; 26:86-92. [PMID: 26595721 DOI: 10.1089/nat.2015.0578] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Preclinical development of RNA interference (RNAi)-based therapeutics requires a rapid, accurate, and robust method of simultaneously quantifying mRNA knockdown in hundreds of samples. The most well-established method to achieve this is quantitative real-time polymerase chain reaction (qRT-PCR), a labor-intensive methodology that requires sample purification, which increases the potential to introduce additional bias. Here, we describe that the QuantiGene(®) branched DNA (bDNA) assay linked to a 96-well Qiagen TissueLyser II is a quick and reproducible alternative to qRT-PCR for quantitative analysis of mRNA expression in vivo directly from tissue biopsies. The bDNA assay is a high-throughput, plate-based, luminescence technique, capable of directly measuring mRNA levels from tissue lysates derived from various biological samples. We have performed a systematic evaluation of this technique for in vivo detection of RNAi-based silencing. We show that similar quality data is obtained from purified RNA and tissue lysates. In general, we observe low intra- and inter-animal variability (around 10% for control samples), and high intermediate precision. This allows minimization of sample size for evaluation of oligonucleotide efficacy in vivo.
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Affiliation(s)
- Andrew H Coles
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Maire F Osborn
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Julia F Alterman
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Anton A Turanov
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Bruno M D C Godinho
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Lori Kennington
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,3 Department of Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Kathryn Chase
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,3 Department of Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Neil Aronin
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,3 Department of Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
| | - Anastasia Khvorova
- 1 RNA Therapeutics Institute, University of Massachusetts Medical School , Worcester, Massachusetts.,2 Department of Molecular Medicine, University of Massachusetts Medical School , Worcester, Massachusetts
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