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McKinzie PB, Bishop ME. A Streamlined and High-Throughput Error-Corrected Next-Generation Sequencing Method for Low Variant Allele Frequency Quantitation. Toxicol Sci 2021; 173:77-85. [PMID: 31621867 DOI: 10.1093/toxsci/kfz221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Quantifying mutant or variable allele frequencies (VAFs) of ≤10-3 using next-generation sequencing (NGS) has utility in both clinical and nonclinical settings. Two common approaches for quantifying VAFs using NGS are tagged single-strand sequencing and duplex sequencing. While duplex sequencing is reported to have sensitivity up to 10-8 VAF, it is not a quick, easy, or inexpensive method. We report a method for quantifying VAFs that are ≥10-4 that is as easy and quick for processing samples as standard sequencing kits, yet less expensive than the kits. The method was developed using PCR fragment-based VAFs of Kras codon 12 in log10 increments from 10-5 to 10-1, then applied and tested on native genomic DNA. For both sources of DNA, there is a proportional increase in the observed VAF to input VAF from 10-4 to 100% mutant samples. Variability of quantitation was evaluated within experimental replicates and shown to be consistent across sample preparations. The error at each successive base read was evaluated to determine if there is a limit of read length for quantitation of ≥10-4, and it was determined that read lengths up to 70 bases are reliable for quantitation. The method described here is adaptable to various oncogene or tumor suppressor gene targets, with the potential to implement multiplexing at the initial tagging step. While easy to perform manually, it is also suited for robotic handling and batch processing of samples, facilitating detection and quantitation of genetic carcinogenic biomarkers before tumor formation or in normal-appearing tissue.
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Affiliation(s)
- Page B McKinzie
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079
| | - Michelle E Bishop
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079
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2
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Lee J, Arisi I, Puxeddu E, Mramba LK, Amicosante M, Swaisgood CM, Pallante M, Brantly ML, Sköld CM, Saltini C. Bronchoalveolar lavage (BAL) cells in idiopathic pulmonary fibrosis express a complex pro-inflammatory, pro-repair, angiogenic activation pattern, likely associated with macrophage iron accumulation. PLoS One 2018; 13:e0194803. [PMID: 29649237 PMCID: PMC5896901 DOI: 10.1371/journal.pone.0194803] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 03/09/2018] [Indexed: 12/11/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease of unknown cause characterized by alveolar epithelial damage, patchy interstitial fibrosis and diffuse microvascular abnormalities. In IPF, alveolar clustering of iron-laden alveolar macrophages—a common sign of microhemorrhage, has been associated with vascular abnormalities and worsening of pulmonary hypertension. As iron-dependent ROS generation has been shown to induce unrestrained macrophage activation in disease models of vascular damage, we explored alveolar macrophage activation phenotype in IPF patients (n = 16) and healthy controls (CTR, n = 7) by RNA sequencing of bronchoalveolar lavage (BAL) cells. The frequencies of macrophages in BAL cells were 86+4% and 83.4+8% in IPF and CTR groups, respectively (p-value = 0.41). In IPF patients, BAL cells showed increased iron-dependent ROS generation (p-value<0.05 vs CTR). Gene expression analysis showed overrepresentation of Gene Ontology processes/functions and KEGG pathways enriched in upregulated M1-type inflammatory (p-value<0.01), M2-type anti-inflammatory/tissue remodeling (p-value<0.0001), and MTPP-type chronic inflammatory/angiogenic (p-value<0.0001) chemokine and cytokine genes. The ex vivo finding was confirmed by the induction of iron-dependent ROS generation and chemokine/cytokine overexpression of Ccl4, Cxcl10 (M1), Il1rn (M2), Cxcl2, and Cxcl7 (MTPP) in MH-S murine immortalized alveolar macrophages exposed to ferric ammonium citrate in culture (p-value<0.05 vs CTR). The data show alveolar macrophage expression of a pro-inflammatory, tissue remodeling and angiogenic complex activation pattern, suggesting that iron accumulation may play a role in macrophage activation.
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Affiliation(s)
- Jungnam Lee
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Ivan Arisi
- Genomics Facility, European Brain Research Institute, Rome, Italy
| | - Ermanno Puxeddu
- Department of Biomedicine and Prevention, University of Roma “Tor Vergata”, Rome, Italy
| | - Lazarus K. Mramba
- Department of Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Massimo Amicosante
- Department of Biomedicine and Prevention, University of Roma “Tor Vergata”, Rome, Italy
| | - Carmen M. Swaisgood
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Marco Pallante
- Department of Biomedicine and Prevention, University of Roma “Tor Vergata”, Rome, Italy
| | - Mark L. Brantly
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - C. Magnus Sköld
- Department of Medicine, Respiratory Medicine Unit, and Lung-Allergy Clinic, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Cesare Saltini
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Florida College of Medicine, Gainesville, Florida, United States of America
- * E-mail:
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Lu Y, Zhang M, Jiang Q, Yin R, Zhu P, Wang H, Liu Z, Zheng C. RNA Extracted from Formalin-Fixed, Paraffin-Embedded Renal Biopsy Biospecimens: An Evaluation of Alternative Extraction Kits and the Effects of Storage Time. Biopreserv Biobank 2017; 15:396-398. [PMID: 28426236 DOI: 10.1089/bio.2017.0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Yinghui Lu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine , Nanjing, China
| | - Mingchao Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine , Nanjing, China
| | - Qi Jiang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine , Nanjing, China
| | - Ru Yin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine , Nanjing, China
| | - Ping Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine , Nanjing, China
| | - Hongtian Wang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine , Nanjing, China
| | - Zhihong Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine , Nanjing, China
| | - Chunxia Zheng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine , Nanjing, China
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Webster AF, Lambert IB, Yauk CL. Toxicogenomics Case Study: Furan. TOXICOGENOMICS IN PREDICTIVE CARCINOGENICITY 2016. [DOI: 10.1039/9781782624059-00390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Development of pragmatic methodologies for human health risk assessment is required to address current regulatory challenges. We applied three toxicogenomic approaches—quantitative, predictive, and mechanistic—to a case study in mice exposed for 3 weeks to the hepatocarcinogen furan. We modeled the dose response of a variety of transcriptional endpoints and found that they produced benchmark doses similar to the furan-dependent cancer benchmark doses. Meta-analyses showed strong similarity between furan-dependent gene expression changes and those associated with several hepatic pathologies. Molecular pathways facilitated the development of a molecular mode of action for furan-induced hepatocellular carcinogenicity. Finally, we compared transcriptomic profiles derived from formalin-fixed and paraffin-embedded (FFPE) samples with those from high-quality frozen samples to evaluate whether archival samples are a viable option for toxicogenomic studies. The advantage of using FFPE tissues is that they are very well characterized (phenotypically); the disadvantage is that formalin degrades biomacromolecules, including RNA. We found that FFPE samples can be used for toxicogenomics using a ribo-depletion RNA-seq protocol. Our case study demonstrates the utility of toxicogenomics data to human health risk assessment, the potential of archival FFPE tissue samples, and identifies viable strategies toward the reduction of animal usage in chemical testing.
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Affiliation(s)
- A. Francina Webster
- Department of Biology, Carleton University 1125 Colonel By Drive Ottawa ON Canada
- Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture 50 Colombine Driveway Ottawa ON Canada
| | - Iain B. Lambert
- Department of Biology, Carleton University 1125 Colonel By Drive Ottawa ON Canada
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Health Canada, Tunney's Pasture 50 Colombine Driveway Ottawa ON Canada
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Webster AF, Zumbo P, Fostel J, Gandara J, Hester SD, Recio L, Williams A, Wood CE, Yauk CL, Mason CE. Mining the Archives: A Cross-Platform Analysis of Gene Expression Profiles in Archival Formalin-Fixed Paraffin-Embedded Tissues. Toxicol Sci 2015; 148:460-72. [PMID: 26361796 PMCID: PMC4659533 DOI: 10.1093/toxsci/kfv195] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a potentially invaluable resource for transcriptomic research. However, use of FFPE samples in genomic studies has been limited by technical challenges resulting from nucleic acid degradation. Here we evaluated gene expression profiles derived from fresh-frozen (FRO) and FFPE mouse liver tissues preserved in formalin for different amounts of time using 2 DNA microarray protocols and 2 whole-transcriptome sequencing (RNA-seq) library preparation methodologies. The ribo-depletion protocol outperformed the other methods by having the highest correlations of differentially expressed genes (DEGs), and best overlap of pathways, between FRO and FFPE groups. The effect of sample time in formalin (18 h or 3 weeks) on gene expression profiles indicated that test article treatment, not preservation method, was the main driver of gene expression profiles. Meta- and pathway analyses indicated that biological responses were generally consistent for 18 h and 3 week FFPE samples compared with FRO samples. However, clear erosion of signal intensity with time in formalin was evident, and DEG numbers differed by platform and preservation method. Lastly, we investigated the effect of time in paraffin on genomic profiles. Ribo-depletion RNA-seq analysis of 8-, 19-, and 26-year-old control blocks resulted in comparable quality metrics, including expected distributions of mapped reads to exonic, untranslated region, intronic, and ribosomal fractions of the transcriptome. Overall, our results indicate that FFPE samples are appropriate for use in genomic studies in which frozen samples are not available, and that ribo-depletion RNA-seq is the preferred method for this type of analysis in archival and long-aged FFPE samples.
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Affiliation(s)
- A Francina Webster
- *Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada; Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa K1S 5B6, Canada
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065
| | - Jennifer Fostel
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Jorge Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065
| | - Susan D Hester
- Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, North Carolina 27709
| | - Leslie Recio
- ILS, Inc., PO Box 13501, Research Triangle Park, North Carolina 27709
| | - Andrew Williams
- *Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada
| | - Charles E Wood
- Office of Research and Development, US Environmental Protection Agency, Research Triangle Park, North Carolina 27709
| | - Carole L Yauk
- *Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada;
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065; The Feil Family Brain and Mind Research Institute (BMRI), 413 East 69th Street, New York, New York 10021; and The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, 1305 York Avenue, New York, New York 10065
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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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