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Casey C, Fullard JF, Sleator RD. Unravelling the genetic basis of Schizophrenia. Gene 2024; 902:148198. [PMID: 38266791 DOI: 10.1016/j.gene.2024.148198] [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] [Received: 09/01/2023] [Revised: 12/07/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Neuronal development is a highly regulated mechanism that is central to organismal function in animals. In humans, disruptions to this process can lead to a range of neurodevelopmental phenotypes, including Schizophrenia (SCZ). SCZ has a significant genetic component, whereby an individual with an SCZ affected family member is eight times more likely to develop the disease than someone with no family history of SCZ. By examining a combination of genomic, transcriptomic and epigenomic datasets, large-scale 'omics' studies aim to delineate the relationship between genetic variation and abnormal cellular activity in the SCZ brain. Herein, we provide a brief overview of some of the key omics methods currently being used in SCZ research, including RNA-seq, the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and high-throughput chromosome conformation capture (3C) approaches (e.g., Hi-C), as well as single-cell/nuclei iterations of these methods. We also discuss how these techniques are being employed to further our understanding of the genetic basis of SCZ, and to identify associated molecular pathways, biomarkers, and candidate drug targets.
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Affiliation(s)
- Clara Casey
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Roy D Sleator
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland.
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Pouyabahar D, Chung SW, Pezzutti OI, Perciani CT, Wang X, Ma XZ, Jiang C, Camat D, Chung T, Sekhon M, Manuel J, Chen XC, McGilvray ID, MacParland SA, Bader GD. A rat liver cell atlas reveals intrahepatic myeloid heterogeneity. iScience 2023; 26:108213. [PMID: 38026201 PMCID: PMC10651689 DOI: 10.1016/j.isci.2023.108213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 08/20/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
The large size and vascular accessibility of the laboratory rat (Rattus norvegicus) make it an ideal hepatic animal model for diseases that require surgical manipulation. Often, the disease susceptibility and outcomes of inflammatory pathologies vary significantly between strains. This study uses single-cell transcriptomics to better understand the complex cellular network of the rat liver, as well as to unravel the cellular and molecular sources of inter-strain hepatic variation. We generated single-cell and single-nucleus transcriptomic maps of the livers of healthy Dark Agouti and Lewis rat strains and developed a factor analysis-based bioinformatics analysis pipeline to study data covariates, such as strain and batch. Using this approach, we discovered transcriptomic variation within the hepatocyte and myeloid populations that underlie distinct cell states between rat strains. This finding will help provide a reference for future investigations on strain-dependent outcomes of surgical experiment models.
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Affiliation(s)
- Delaram Pouyabahar
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Sai W. Chung
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Olivia I. Pezzutti
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Catia T. Perciani
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xinle Wang
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xue-Zhong Ma
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Chao Jiang
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Damra Camat
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Trevor Chung
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Manmeet Sekhon
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Justin Manuel
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xu-Chun Chen
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Ian D. McGilvray
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Sonya A. MacParland
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Gary D. Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
- Princess Margaret Research Institute, University Health Network, Toronto, ON, Canada
- The Multiscale Human Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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3
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Short-term in vivo testing to discriminate genotoxic carcinogens from non-genotoxic carcinogens and non-carcinogens using next-generation RNA sequencing, DNA microarray, and qPCR. Genes Environ 2023; 45:7. [PMID: 36755350 PMCID: PMC9909887 DOI: 10.1186/s41021-023-00262-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 01/05/2023] [Indexed: 02/10/2023] Open
Abstract
Next-generation RNA sequencing (RNA-Seq) has identified more differentially expressed protein-coding genes (DEGs) and provided a wider quantitative range of expression level changes than conventional DNA microarrays. JEMS·MMS·Toxicogenomics group studied DEGs with targeted RNA-Seq on freshly frozen rat liver tissues and on formalin-fixed paraffin-embedded (FFPE) rat liver tissues after 28 days of treatment with chemicals and quantitative real-time PCR (qPCR) on rat and mouse liver tissues after 4 to 48 h treatment with chemicals and analyzed by principal component analysis (PCA) as statics. Analysis of rat public DNA microarray data (Open TG-GATEs) was also performed. In total, 35 chemicals were analyzed [15 genotoxic hepatocarcinogens (GTHCs), 9 non-genotoxic hepatocarcinogens (NGTHCs), and 11 non-genotoxic non-hepatocarcinogens (NGTNHCs)]. As a result, 12 marker genes (Aen, Bax, Btg2, Ccnf, Ccng1, Cdkn1a, Gdf15, Lrp1, Mbd1, Phlda3, Plk2, and Tubb4b) were proposed to discriminate GTHCs from NGTHCs and NGTNHCs. U.S. Environmental Protection Agency studied DEGs induced by 4 known GTHCs in rat liver using DNA microarray and proposed 7 biomarker genes, Bax, Bcmp1, Btg2, Ccng1, Cdkn1a, Cgr19, and Mgmt for GTHCs. Studies involving the use of whole-transcriptome RNA-Seq upon exposure to chemical carcinogens in vivo have also been performed in rodent liver, kidney, lung, colon, and other organs, although discrimination of GTHCs from NGTHCs was not examined. Candidate genes published using RNA-Seq, qPCR, and DNA microarray will be useful for the future development of short-term in vivo studies of environmental carcinogens using RNA-Seq.
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Iori S, Pauletto M, Bassan I, Bonsembiante F, Gelain ME, Bardhi A, Barbarossa A, Zaghini A, Dacasto M, Giantin M. Deepening the Whole Transcriptomics of Bovine Liver Cells Exposed to AFB1: A Spotlight on Toll-like Receptor 2. Toxins (Basel) 2022; 14:toxins14070504. [PMID: 35878242 PMCID: PMC9323327 DOI: 10.3390/toxins14070504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 12/13/2022] Open
Abstract
Aflatoxin B1 (AFB1) is a food contaminant metabolized mostly in the liver and leading to hepatic damage. Livestock species are differently susceptible to AFB1, but the underlying mechanisms of toxicity have not yet been fully investigated, especially in ruminants. Thus, the aim of the present study was to better characterize the molecular mechanism by which AFB1 exerts hepatotoxicity in cattle. The bovine fetal hepatocyte cell line (BFH12) was exposed for 48 h to three different AFB1 concentrations (0.9 µM, 1.8 µM and 3.6 µM). Whole-transcriptomic changes were measured by RNA-seq analysis, showing significant differences in the expression of genes mainly involved in inflammatory response, oxidative stress, drug metabolism, apoptosis and cancer. As a confirmatory step, post-translational investigations on genes of interest were implemented. Cell death associated with necrosis rather than apoptosis events was noted. As far as the toxicity mechanism is concerned, a molecular pathway linking inflammatory response and oxidative stress was postulated. Toll-Like Receptor 2 (TLR2) activation, consequent to AFB1 exposure, triggers an intracellular signaling cascade involving a kinase (p38β MAPK), which in turn allows the nuclear translocation of the activator protein-1 (AP-1) and NF-κB, finally leading to the release of pro-inflammatory cytokines. Furthermore, a p38β MAPK negative role in cytoprotective genes regulation was postulated. Overall, our investigations improved the actual knowledge on the molecular effects of this worldwide relevant natural toxin in cattle.
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Affiliation(s)
- Silvia Iori
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, Legnaro, 35020 Padua, Italy; (S.I.); (M.P.); (I.B.); (F.B.); (M.E.G.); (M.D.)
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, Legnaro, 35020 Padua, Italy; (S.I.); (M.P.); (I.B.); (F.B.); (M.E.G.); (M.D.)
| | - Irene Bassan
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, Legnaro, 35020 Padua, Italy; (S.I.); (M.P.); (I.B.); (F.B.); (M.E.G.); (M.D.)
| | - Federico Bonsembiante
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, Legnaro, 35020 Padua, Italy; (S.I.); (M.P.); (I.B.); (F.B.); (M.E.G.); (M.D.)
- Department of Animal Medicine, Production and Health, University of Padua, Viale dell’Università 16, Legnaro, 35020 Padua, Italy
| | - Maria Elena Gelain
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, Legnaro, 35020 Padua, Italy; (S.I.); (M.P.); (I.B.); (F.B.); (M.E.G.); (M.D.)
| | - Anisa Bardhi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Via Tolara di Sopra 50, Ozzano dell’Emilia, 40064 Bologna, Italy; (A.B.); (A.B.); (A.Z.)
| | - Andrea Barbarossa
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Via Tolara di Sopra 50, Ozzano dell’Emilia, 40064 Bologna, Italy; (A.B.); (A.B.); (A.Z.)
| | - Anna Zaghini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Via Tolara di Sopra 50, Ozzano dell’Emilia, 40064 Bologna, Italy; (A.B.); (A.B.); (A.Z.)
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, Legnaro, 35020 Padua, Italy; (S.I.); (M.P.); (I.B.); (F.B.); (M.E.G.); (M.D.)
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale dell’Università 16, Legnaro, 35020 Padua, Italy; (S.I.); (M.P.); (I.B.); (F.B.); (M.E.G.); (M.D.)
- Correspondence: ; Tel.: +39-049-827-2946
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El-Dairi R, Rysä J, Storvik M, Pasanen M, Huuskonen P. Aflatoxin B1 targeted gene expression profiles in human placental primary trophoblast cells. Curr Res Toxicol 2022; 3:100082. [PMID: 35814288 PMCID: PMC9263407 DOI: 10.1016/j.crtox.2022.100082] [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: 12/31/2021] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/25/2022] Open
Abstract
Gene expression profiles were studied in human primary trophoblast cells. 170 genes were significantly dysregulated in aflatoxin B1-exposed trophoblasts. AhR-mediated estrogen receptor signalling was dysregulated in response to AFB1. Transcripts involved in endocrine signalling and energy homeostasis were disrupted. Cellular growth and development, cell cycle and DNA repair processes were affected.
Aflatoxin B1 (AFB1) is a mycotoxin produced by Aspergillus flavus and A. parasiticus. A high exposure (40 nM and 1 µM AFB1 for 72 h) was used to study mechanistic effects of AFB1 on gene expression patterns in human primary trophoblast cells, isolated from full term placentae after delivery. Gene expression profiling was conducted, and Ingenuity pathway analysis (IPA) software was used to identify AFB1-regulated gene networks and regulatory pathways. In response to 40 nM AFB1, only 7 genes were differentially expressed whereas 1 µM AFB1 significantly dysregulated 170 genes (124 down- and 46 upregulated, ±1.5-fold, p < 0.05) in AFB1-exposed trophoblasts when compared to controls. The top downregulated genes were involved in endocrine signalling and biosynthesis of hormones, and lipid and carbohydrate metabolism. The top upregulated genes were involved in protein synthesis and regulation of cell cycle. The main canonical pathways identified by IPA were associated with endocrine signalling including growth hormone signalling, and corticotropin releasing hormone signalling. Furthermore, genes involved in aryl hydrocarbon receptor (AhR)-mediated estrogen receptor signalling were dysregulated in response to AFB1. Our findings indicate that a high concentration 72 h AFB1 exposure caused relatively moderate number of changes on transcript level to human placental primary trophoblast cells. However, these preliminary results need to be confirmed with human-relevant concentrations of AFB1.
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Gaine ME, Bahl E, Chatterjee S, Michaelson JJ, Abel T, Lyons LC. Altered hippocampal transcriptome dynamics following sleep deprivation. Mol Brain 2021; 14:125. [PMID: 34384474 PMCID: PMC8361790 DOI: 10.1186/s13041-021-00835-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Widespread sleep deprivation is a continuing public health problem in the United States and worldwide affecting adolescents and adults. Acute sleep deprivation results in decrements in spatial memory and cognitive impairments. The hippocampus is vulnerable to acute sleep deprivation with changes in gene expression, cell signaling, and protein synthesis. Sleep deprivation also has long lasting effects on memory and performance that persist after recovery sleep, as seen in behavioral studies from invertebrates to humans. Although previous research has shown that acute sleep deprivation impacts gene expression, the extent to which sleep deprivation affects gene regulation remains unknown. Using an unbiased deep RNA sequencing approach, we investigated the effects of acute sleep deprivation on gene expression in the hippocampus. We identified 1,146 genes that were significantly dysregulated following sleep deprivation with 507 genes upregulated and 639 genes downregulated, including protein coding genes and long non-coding RNAs not previously identified as impacted by sleep deprivation. Notably, genes significantly upregulated after sleep deprivation were associated with RNA splicing and the nucleus. In contrast, downregulated genes were associated with cell adhesion, dendritic localization, the synapse, and postsynaptic membrane. Furthermore, we found through independent experiments analyzing a subset of genes that three hours of recovery sleep following acute sleep deprivation was sufficient to normalize mRNA abundance for most genes, although exceptions occurred for some genes that may affect RNA splicing or transcription. These results clearly demonstrate that sleep deprivation differentially regulates gene expression on multiple transcriptomic levels to impact hippocampal function.
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Affiliation(s)
- Marie E Gaine
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Pharmaceutical Sciences and Experimental Therapeutics (PSET), College of Pharmacy, University of Iowa, Iowa City, IA, USA
| | - Ethan Bahl
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, USA
| | - Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Jacob J Michaelson
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Biomedical Engineering, College of Engineering, University of Iowa, Iowa City, IA, USA
- Department of Communication Sciences and Disorders, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA, USA
- Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Lisa C Lyons
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL, USA.
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7
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Development of an on-spot and rapid recombinase polymerase amplification assay for Aspergillus flavus detection in grains. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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8
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Baltussen TJH, Coolen JPM, Verweij PE, Dijksterhuis J, Melchers WJG. Identifying Conserved Generic Aspergillus spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics. J Fungi (Basel) 2021; 7:270. [PMID: 33916245 PMCID: PMC8067318 DOI: 10.3390/jof7040270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/27/2021] [Accepted: 03/29/2021] [Indexed: 12/26/2022] Open
Abstract
Aspergillus spp. is an opportunistic human pathogen that may cause a spectrum of pulmonary diseases. In order to establish infection, inhaled conidia must germinate, whereby they break dormancy, start to swell, and initiate a highly polarized growth process. To identify critical biological processes during germination, we performed a cross-platform, cross-species comparative analysis of germinating A. fumigatus and A. niger conidia using transcriptional data from published RNA-Seq and Affymetrix studies. A consensus co-expression network analysis identified four gene modules associated with stages of germination. These modules showed numerous shared biological processes between A. niger and A. fumigatus during conidial germination. Specifically, the turquoise module was enriched with secondary metabolism, the black module was highly enriched with protein synthesis, the darkgreen module was enriched with protein fate, and the blue module was highly enriched with polarized growth. More specifically, enriched functional categories identified in the blue module were vesicle formation, vesicular transport, tubulin dependent transport, actin-dependent transport, exocytosis, and endocytosis. Genes important for these biological processes showed similar expression patterns in A. fumigatus and A. niger, therefore, they could be potential antifungal targets. Through cross-platform, cross-species comparative analysis, we were able to identify biologically meaningful modules shared by A. fumigatus and A. niger, which underscores the potential of this approach.
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Affiliation(s)
- Tim J. H. Baltussen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Paul E. Verweij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Institute, 3584 CT Utrecht, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (J.P.M.C.); (P.E.V.); (W.J.G.M.)
- Center of Expertise in Mycology Radboudumc/CWZ, 6532 SZ Nijmegen, The Netherlands
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9
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Selvaraju S, Ramya L, Parthipan S, Swathi D, Binsila BK, Kolte AP. Deciphering the complexity of sperm transcriptome reveals genes governing functional membrane and acrosome integrities potentially influence fertility. Cell Tissue Res 2021; 385:207-222. [PMID: 33783607 DOI: 10.1007/s00441-021-03443-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/01/2021] [Indexed: 12/14/2022]
Abstract
Deciphering sperm transcriptome is the key to understanding the molecular mechanisms governing peri-fertilization, embryonic development, and pregnancy establishment. This study aimed to profile sperm transcriptome to identify signature transcripts regulating male fertility. Semen samples were collected from 47 bulls with varied fertility rates. The sperm total RNA was isolated (n = 8) and subjected to transcriptome sequencing. Based on the expression pattern obtained from RNA profiling, the bulls were grouped (p = 0.03) into high-fertile and sub-fertile, and signature transcripts controlling sperm functions and fertility were identified. The results were validated using the OMIM database, qPCR, and sperm function tests. The sperm contains 1100 to 1700 intact transcripts, of which BCL2L11 and CAPZA3 were abundant and associated (p < 0.05) with spermatogenesis and post-embryonic organ morphogenesis. The upregulated genes in the acrosome integrity and functional membrane integrity groups had a close association with the fertility rate. The biological functions of these upregulated genes (p < 0.05) in the high-fertile bulls were associated with spermatogenesis (AFF4 and BRIP1), sperm motility (AK6 and ATP6V1G3), capacitation and zona binding (AGFG1), embryo development (TCF7 and AKIRIN2), and placental development (KRT19). The transcripts involved in pathways regulating embryonic development such as translation (EEF1B2 and MTIF3, p = 8.87E-05) and nonsense-mediated decay (RPL23 and RPL7A, p = 5.01E-27) were upregulated in high-fertile bulls. The identified transcripts may significantly impact oocyte function, embryogenesis, trophectoderm development, and pregnancy establishment. In addition, the study also reveals that the genes governing sperm functional membrane integrity and acrosome integrity have a prospective effect on male fertility.
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Affiliation(s)
- Sellappan Selvaraju
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India.
| | - Laxman Ramya
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Sivashanmugam Parthipan
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Divakar Swathi
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Bala Krishnan Binsila
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Atul P Kolte
- Omics Laboratory, Animal Nutrition Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
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10
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Li D, Gong B, Xu J, Ning B, Tong W. Impact of Sequencing Depth and Library Preparation on Toxicological Interpretation of RNA-Seq Data in a "Three-Sample" Scenario. Chem Res Toxicol 2021; 34:529-540. [PMID: 33354967 PMCID: PMC7887111 DOI: 10.1021/acs.chemrestox.0c00368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
While RNA-sequencing (RNA-seq) has emerged as a standard approach in toxicogenomics, its full potential in gaining underlying toxicological mechanisms is still not clear when only three biological replicates are used. This "three-sample" study design is common in toxicological research, particularly in animal studies during preclinical drug development. Sequencing depth (the total number of reads in an experiment) and library preparation are critical to the resolution and integrity of RNA-seq data and biological interpretation. We used aflatoxin b1 (AFB1), a model toxicant, to investigate the effect of sequencing depth and library preparation in RNA-seq on toxicological interpretation in the "three-sample" scenario. We also compared different gene profiling platforms (RNA-seq, TempO-seq, microarray, and qPCR) using identical liver samples. Well-established mechanisms of AFB1 toxicity served as ground truth for our comparative analyses. We found that a minimum of 20 million reads was sufficient to elicit key toxicity functions and pathways underlying AFB1-induced liver toxicity using three replicates and that identification of differentially expressed genes was positively associated with sequencing depth to a certain extent. Further, our results showed that RNA-seq revealed toxicological insights from pathway enrichment with overall higher statistical power and overlap ratio, compared with TempO-seq and microarray. Moreover, library preparation using the same methods was important to reproducing the toxicological interpretation.
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Affiliation(s)
- Dongying Li
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas 72079, United States
| | - Binsheng Gong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas 72079, United States
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas 72079, United States
| | - Baitang Ning
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas 72079, United States
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas 72079, United States
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11
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Yang H, Li Y, Jin Y, Kan L, Shen C, Malladi A, Nambeesan S, Xu Y, Dong C. Transcriptome Analysis of Pyrus betulaefolia Seedling Root Responses to Short-Term Potassium Deficiency. Int J Mol Sci 2020; 21:E8857. [PMID: 33238495 PMCID: PMC7700257 DOI: 10.3390/ijms21228857] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/02/2022] Open
Abstract
Potassium (K) plays a crucial role in multiple physiological and developmental processes in plants. Its deficiency is a common abiotic stress that inhibits plant growth and reduces crop productivity. A better understanding of the mechanisms involved in plant responses to low K could help to improve the efficiency of K use in plants. However, such responses remain poorly characterized in fruit tree species such as pears (Pyrus sp). We analyzed the physiological and transcriptome responses of a commonly used pear rootstock, Pyrus betulaefolia, to K-deficiency stress (0 mM). Potassium deprivation resulted in apparent changes in root morphology, with short-term low-K stress resulting in rapidly enhanced root growth. Transcriptome analyses indicated that the root transcriptome was coordinately altered within 6 h after K deprivation, a process that continued until 15 d after treatment. Potassium deprivation resulted in the enhanced expression (up to 5-fold) of a putative high-affinity K+ transporter, PbHAK5 (Pbr037826.1), suggesting the up-regulation of mechanisms associated with K+ acquisition. The enhanced root growth in response to K-deficiency stress was associated with a rapid and sustained decrease in the expression of a transcription factor, PbMYB44 (Pbr015309.1), potentially involved in mediating auxin responses, and the increased expression of multiple genes associated with regulating root growth. The concentrations of several phytohormones including indoleacetic acid (IAA), ABA, ETH, gibberellin (GA3), and jasmonic acid (JA) were higher in response to K deprivation. Furthermore, genes coding for enzymes associated with carbon metabolism such as SORBITOL DEHYDROGENASE (SDH) and SUCROSE SYNTHASE (SUS) displayed greatly enhanced expression in the roots under K deprivation, presumably indicating enhanced metabolism to meet the increased energy demands for growth and K+ acquisition. Together, these data suggest that K deprivation in P. betulaefolia results in the rapid re-programming of the transcriptome to enhance root growth and K+ acquisition. These data provide key insights into the molecular basis for understanding low-K-tolerance mechanisms in pears and in other related fruit trees and identifying potential candidates that warrant further analyses.
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Affiliation(s)
- Han Yang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (H.Y.); (Y.J.); (L.K.); (Y.X.)
| | - Yan Li
- College of Life Science, Hubei Engineering University, Xiaogan 432100, China;
| | - Yumeng Jin
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (H.Y.); (Y.J.); (L.K.); (Y.X.)
| | - Liping Kan
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (H.Y.); (Y.J.); (L.K.); (Y.X.)
| | - Changwei Shen
- School of Resources and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang 453003, China;
| | - Anish Malladi
- Department of Horticulture, 1111 Miller Plant Sciences, University of Georgia, Athens, GA 30602, USA; (A.M.); (S.N.)
| | - Savithri Nambeesan
- Department of Horticulture, 1111 Miller Plant Sciences, University of Georgia, Athens, GA 30602, USA; (A.M.); (S.N.)
| | - Yangchun Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (H.Y.); (Y.J.); (L.K.); (Y.X.)
| | - Caixia Dong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, China; (H.Y.); (Y.J.); (L.K.); (Y.X.)
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12
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Choi SY, Kim TH, Hong MW, Park TS, Lee H, Lee SJ. Transcriptomic alterations induced by aflatoxin B1 and ochratoxin A in LMH cell line. Poult Sci 2020; 99:5265-5274. [PMID: 33142442 PMCID: PMC7647754 DOI: 10.1016/j.psj.2020.05.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/09/2020] [Accepted: 05/22/2020] [Indexed: 12/23/2022] Open
Abstract
Aflatoxin B1 (AFB1) and ochratoxin A (OTA), which are toxic metabolites of ubiquitously occurring molds, show diverse toxicological effects such as hepatotoxicity, genotoxicity, and immunotoxicity in human and animals. Despite poultry show sensitivity to AFB1 and OTA, the mechanism of these mycotoxins in chickens has not been fully investigated. Here, we aimed to elucidate the molecular mechanism induced by AFB1 and/or OTA in chicken hepatic cells using transcriptomic analysis. Aflatoxin B1 and OTA induced cytotoxic effects in a dose-dependent manner at 48 h after exposure. Furthermore, correlation effect indicated an antagonism between the 2 toxins. The mRNA sequencing of AFB1-treated or OTA-treated chicken hepatocarcinoma and functional analysis revealed the pathways that were commonly regulated by both mycotoxins, especially PPAR signaling, focal adhesion, and MAPK signaling. Based on these findings, a possible hypothesis is that AFB1 and OTA have similar toxic mechanisms and compete for some steps in the chicken liver, and it is expected that the mycotoxins would have antagonistic effects. In addition, genes identified through transcriptome analysis provide candidates for further study of AFB1 and OTA toxicity and targets for efforts to improve the health of chickens exposed to mycotoxins.
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Affiliation(s)
- So-Young Choi
- Department of Animal Life Science, Kangwon National University, Chuncheon-si, Gangwon-do 24341, Korea
| | - Tae Hyun Kim
- Department of Animal Science, University of California, Davis, Davis, CA 95616, USA
| | - Min-Wook Hong
- Department of Animal Life Science, Kangwon National University, Chuncheon-si, Gangwon-do 24341, Korea
| | - Tae Sub Park
- Graduate School of International Agricultural Technology and Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang-gun, Gangwon-do 25354, Korea
| | - Hyojeong Lee
- Department of Animal Life Science, Kangwon National University, Chuncheon-si, Gangwon-do 24341, Korea
| | - Sung-Jin Lee
- Department of Animal Life Science, Kangwon National University, Chuncheon-si, Gangwon-do 24341, Korea.
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13
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Angata K, Sawaki H, Tsujikawa S, Ocho M, Togayachi A, Narimatsu H. Glycogene Expression Profiling of Hepatic Cells by RNA-Seq Analysis for Glyco-Biomarker Identification. Front Oncol 2020; 10:1224. [PMID: 32850363 PMCID: PMC7402167 DOI: 10.3389/fonc.2020.01224] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/15/2020] [Indexed: 01/01/2023] Open
Abstract
Glycans are primarily generated by “glycogenes,” which consist of more than 200 genes for glycosynthesis, including sugar-nucleotide synthases, sugar-nucleotide transporters, and glycosyltransferases. Measuring the expression level of glycogenes is one of the approaches to analyze the glycomes of particular biological and clinical samples. To develop an effective strategy for identifying the glycosylated biomarkers, we performed transcriptome analyses using quantitative real-time polymerase chain reaction (qRT-PCR) arrays and RNA sequencing (RNA-Seq). First, we measured and analyzed the transcriptome from the primary culture of human liver cells and hepatocarcinoma cells using RNA-Seq. This analysis revealed similar but distinctive expression profiles of glycogenes among hepatic cells as indicated by the qRT-PCR arrays, which determined a copy number of 186 glycogenes. Both data sets indicated that altered expression of glycosyltransferases affect the glycosylation of particular glycoproteins, which is consistent with the mass analysis data. Moreover, RNA-Seq analysis can uncover mutations in glycogenes and search differently expressed genes out of more than 50,000 distinct human gene transcripts including candidate biomarkers that were previously reported for hepatocarcinoma cells. Identification of candidate glyco-biomarkers from the expression profile of the glycogenes and proteins from liver cancer tissues available from public database emphasized the possibility that even though the expression level of biomarkers might not be altered, the expression of the glycogenes modifying biomarkers, generating glyco-biomarkers, might be different. Pathway analysis revealed that ~20% of the glycogenes exhibited different expression levels in normal and cancer cells. Thus, transcriptome analyses using both qRT-PCR array and RNA-Seq in combination with glycome and glycoproteome analyses can be advantageous to identify “glyco-biomarkers” by reinforcing information at the expression levels of both glycogenes and proteins.
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Affiliation(s)
- Kiyohiko Angata
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hiromichi Sawaki
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Shigeko Tsujikawa
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Makoto Ocho
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Akira Togayachi
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hisashi Narimatsu
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
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14
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Mellors T, Withers JB, Ameli A, Jones A, Wang M, Zhang L, Sanchez HN, Santolini M, Do Valle I, Sebek M, Cheng F, Pappas DA, Kremer JM, Curtis JR, Johnson KJ, Saleh A, Ghiassian SD, Akmaev VR. Clinical Validation of a Blood-Based Predictive Test for Stratification of Response to Tumor Necrosis Factor Inhibitor Therapies in Rheumatoid Arthritis Patients. NETWORK AND SYSTEMS MEDICINE 2020. [DOI: 10.1089/nsm.2020.0007] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
| | | | - Asher Ameli
- Scipher Medicine, Waltham, Massachusetts, USA
| | - Alex Jones
- Scipher Medicine, Waltham, Massachusetts, USA
| | | | - Lixia Zhang
- Scipher Medicine, Waltham, Massachusetts, USA
| | | | - Marc Santolini
- Center for Research and Interdisciplinarity (CRI), University Paris Descartes, Paris, France
| | - Italo Do Valle
- Center for Complex Network Research, Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Michael Sebek
- Center for Complex Network Research, Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Feixiong Cheng
- Center for Complex Network Research, Department of Physics, Northeastern University, Boston, Massachusetts, USA
| | - Dimitrios A. Pappas
- Division of Rheumatology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
- CORRONA, LCC, Waltham, Massachusetts, USA
| | - Joel M. Kremer
- CORRONA, LCC, Waltham, Massachusetts, USA
- Albany Medical College, The Center for Rheumatology, Albany, New York, USA
| | - Jeffery R. Curtis
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Alif Saleh
- Scipher Medicine, Waltham, Massachusetts, USA
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15
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Insights into Aflatoxin B1 Toxicity in Cattle: An In Vitro Whole-Transcriptomic Approach. Toxins (Basel) 2020; 12:toxins12070429. [PMID: 32610656 PMCID: PMC7404968 DOI: 10.3390/toxins12070429] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 02/07/2023] Open
Abstract
Aflatoxins, and particularly aflatoxin B1 (AFB1), are toxic mycotoxins to humans and farm animal species, resulting in acute and chronic toxicities. At present, AFB1 is still considered a global concern with negative impacts on health, the economy, and social life. In farm animals, exposure to AFB1-contaminated feed may cause several untoward effects, liver damage being one of the most devastating ones. In the present study, we assessed in vitro the transcriptional changes caused by AFB1 in a bovine fetal hepatocyte-derived cell line (BFH12). To boost the cellular response to AFB1, cells were pre-treated with the co-planar PCB 3,3′,4,4′,5-pentachlorobiphenyl (PCB126), a known aryl hydrocarbon receptor agonist. Three experimental groups were considered: cells exposed to the vehicle only, to PCB126, and to PCB126 and AFB1. A total of nine RNA-seq libraries (three replicates/group) were constructed and sequenced. The differential expression analysis showed that PCB126 induced only small transcriptional changes. On the contrary, AFB1 deeply affected the cell transcriptome, the majority of significant genes being associated with cancer, cellular damage and apoptosis, inflammation, bioactivation, and detoxification pathways. Investigating mRNA perturbations induced by AFB1 in cattle BFH12 cells will help us to better understand AFB1 toxicodynamics in this susceptible and economically important food-producing species.
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16
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Merrick BA, Phadke DP, Bostrom MA, Shah RR, Wright GM, Wang X, Gordon O, Pelch KE, Auerbach SS, Paules RS, DeVito MJ, Waalkes MP, Tokar EJ. KRAS-retroviral fusion transcripts and gene amplification in arsenic-transformed, human prostate CAsE-PE cancer cells. Toxicol Appl Pharmacol 2020; 397:115017. [PMID: 32344290 PMCID: PMC7606314 DOI: 10.1016/j.taap.2020.115017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/16/2020] [Accepted: 04/19/2020] [Indexed: 01/03/2023]
Abstract
CAsE-PE cells are an arsenic-transformed, human prostate epithelial line containing oncogenic mutations in KRAS compared to immortalized, normal KRAS parent cells, RWPE-1. We previously reported increased copy number of mutated KRAS in CAsE-PE cells, suggesting gene amplification. Here, KRAS flanking genomic and transcriptomic regions were sequenced in CAsE-PE cells for insight into KRAS amplification. Comparison of DNA-Seq and RNA-Seq showed increased reads from background aligning to all KRAS exons in CAsE-PE cells, while a uniform DNA-Seq read distribution occurred in RWPE-1 cells with normal transcript expression. We searched for KRAS fusions in DNA and RNA sequencing data finding a portion of reads aligning to KRAS and viral sequence. After generation of cDNA from total RNA, short and long KRAS probes were generated to hybridize cDNA and KRAS enriched fragments were PacBio sequenced. More KRAS reads were captured from CAsE-PE cDNA versus RWPE-1 by each probe set. Only CAsE-PE cDNA showed KRAS viral fusion transcripts, primarily mapping to LTR and endogenous retrovirus sequences on either 5'- or 3'-ends of KRAS. Most KRAS viral fusion transcripts contained 4 to 6 exons but some PacBio sequences were in unusual orientations, suggesting viral insertions within the gene body. Additionally, conditioned media was extracted for potential retroviral particles. RNA-Seq of culture media isolates identified KRAS retroviral fusion transcripts in CAsE-PE media only. Truncated KRAS transcripts suggested multiple retroviral integration sites occurred within the KRAS gene producing KRAS retroviral fusions of various lengths. Findings suggest activation of endogenous retroviruses in arsenic carcinogenesis should be explored.
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Affiliation(s)
- B Alex Merrick
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States.
| | - Dhiral P Phadke
- Sciome, LLC, Research Triangle Park, North Carolina, United States
| | - Meredith A Bostrom
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States
| | - Ruchir R Shah
- Sciome, LLC, Research Triangle Park, North Carolina, United States
| | - Garron M Wright
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States
| | - Xinguo Wang
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States
| | - Oksana Gordon
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States
| | - Katherine E Pelch
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Scott S Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Richard S Paules
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Michael J DeVito
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Michael P Waalkes
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
| | - Erik J Tokar
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States
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17
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Zhao W, Quansah E, Yuan M, Gou Q, Mengal K, Li P, Wu S, Xu C, Yi C, Cai X. Region-specific gene expression in the epididymis of Yak. Theriogenology 2019; 139:132-146. [DOI: 10.1016/j.theriogenology.2019.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 08/02/2019] [Accepted: 08/02/2019] [Indexed: 12/25/2022]
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18
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Arenas-Huertero F, Zaragoza-Ojeda M, Sánchez-Alarcón J, Milić M, Šegvić Klarić M, Montiel-González JM, Valencia-Quintana R. Involvement of Ahr Pathway in Toxicity of Aflatoxins and Other Mycotoxins. Front Microbiol 2019; 10:2347. [PMID: 31681212 PMCID: PMC6798329 DOI: 10.3389/fmicb.2019.02347] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/26/2019] [Indexed: 12/18/2022] Open
Abstract
The purpose of this review is to present information about the role of activation of aflatoxins and other mycotoxins, of the aryl hydrocarbon receptor (AhR) pathway. Aflatoxins and other mycotoxins are a diverse group of secondary metabolites that can be contaminants in a broad range of agricultural products and feeds. Some species of Aspergillus, Alternaria, Penicilium, and Fusarium are major producers of mycotoxins, some of which are toxic and carcinogenic. Several aflatoxins are planar molecules that can activate the AhR. AhR participates in the detoxification of several xenobiotic substances and activates phase I and phase II detoxification pathways. But it is important to recognize that AhR activation also affects differentiation, cell adhesion, proliferation, and immune response among others. Any examination of the effects of aflatoxins and other toxins that act as activators to AhR must consider the potential of the disruption of several cellular functions in order to extend the perception thus far about the toxic and carcinogenic effects of these toxins. There have been no Reviews of existing data between the relation of AhR and aflatoxins and this one attempts to give information precisely about this dichotomy.
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Affiliation(s)
- Francisco Arenas-Huertero
- Experimental Pathology Research Laboratory, Children’s Hospital of Mexico Federico Gómez, Mexico, Mexico
| | - Montserrat Zaragoza-Ojeda
- Experimental Pathology Research Laboratory, Children’s Hospital of Mexico Federico Gómez, Mexico, Mexico
| | - Juana Sánchez-Alarcón
- Rafael Villalobos-Pietrini Laboratory of Genomic Toxicology and Environmental Chemistry, Faculty of Agrobiology, Autonomous University of Tlaxcala, Tlaxcala, Mexico
| | - Mirta Milić
- Mutagenesis Unit, Institute for Medical Research and Occupational Health, Zagreb, Croatia
| | - Maja Šegvić Klarić
- Department of Microbiology, Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - José M. Montiel-González
- Rafael Villalobos-Pietrini Laboratory of Genomic Toxicology and Environmental Chemistry, Faculty of Agrobiology, Autonomous University of Tlaxcala, Tlaxcala, Mexico
| | - Rafael Valencia-Quintana
- Rafael Villalobos-Pietrini Laboratory of Genomic Toxicology and Environmental Chemistry, Faculty of Agrobiology, Autonomous University of Tlaxcala, Tlaxcala, Mexico
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19
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Merrick BA, Phadke DP, Bostrom MA, Shah RR, Wright GM, Wang X, Gordon O, Pelch KE, Auerbach SS, Paules RS, DeVito MJ, Waalkes MP, Tokar EJ. Arsenite malignantly transforms human prostate epithelial cells in vitro by gene amplification of mutated KRAS. PLoS One 2019; 14:e0215504. [PMID: 31009485 PMCID: PMC6476498 DOI: 10.1371/journal.pone.0215504] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/04/2019] [Indexed: 12/20/2022] Open
Abstract
Inorganic arsenic is an environmental human carcinogen of several organs including the urinary tract. RWPE-1 cells are immortalized, non-tumorigenic, human prostate epithelia that become malignantly transformed into the CAsE-PE line after continuous in vitro exposure to 5μM arsenite over a period of months. For insight into in vitro arsenite transformation, we performed RNA-seq for differential gene expression and targeted sequencing of KRAS. We report >7,000 differentially expressed transcripts in CAsE-PE cells compared to RWPE-1 cells at >2-fold change, q<0.05 by RNA-seq. Notably, KRAS expression was highly elevated in CAsE-PE cells, with pathway analysis supporting increased cell proliferation, cell motility, survival and cancer pathways. Targeted DNA sequencing of KRAS revealed a mutant specific allelic imbalance, ‘MASI’, frequently found in primary clinical tumors. We found high expression of a mutated KRAS transcript carrying oncogenic mutations at codons 12 and 59 and many silent mutations, accompanied by lower expression of a wild-type allele. Parallel cultures of RWPE-1 cells retained a wild-type KRAS genotype. Copy number analysis and sequencing showed amplification of the mutant KRAS allele. KRAS is expressed as two splice variants, KRAS4a and KRAS4b, where variant 4b is more prevalent in normal cells compared to greater levels of variant 4a seen in tumor cells. 454 Roche sequencing measured KRAS variants in each cell type. We found KRAS4a as the predominant transcript variant in CAsE-PE cells compared to KRAS4b, the variant expressed primarily in RWPE-1 cells and in normal prostate, early passage, primary epithelial cells. Overall, gene expression data were consistent with KRAS-driven proliferation pathways found in spontaneous tumors and malignantly transformed cell lines. Arsenite is recognized as an important environmental carcinogen, but it is not a direct mutagen. Further investigations into this in vitro transformation model will focus on genomic events that cause arsenite-mediated mutation and overexpression of KRAS in CAsE-PE cells.
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Affiliation(s)
- B. Alex Merrick
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
- * E-mail:
| | - Dhiral P. Phadke
- Sciome, LLC, Research Triangle Park, North Carolina, United States of America
| | - Meredith A. Bostrom
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States of America
| | - Ruchir R. Shah
- Sciome, LLC, Research Triangle Park, North Carolina, United States of America
| | - Garron M. Wright
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States of America
| | - Xinguo Wang
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States of America
| | - Oksana Gordon
- David H. Murdock Research Institute, Kannapolis, North Carolina, United States of America
| | - Katherine E. Pelch
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Scott S. Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Richard S. Paules
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Michael J. DeVito
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Michael P. Waalkes
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Erik J. Tokar
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
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20
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Rao MS, Van Vleet TR, Ciurlionis R, Buck WR, Mittelstadt SW, Blomme EAG, Liguori MJ. Comparison of RNA-Seq and Microarray Gene Expression Platforms for the Toxicogenomic Evaluation of Liver From Short-Term Rat Toxicity Studies. Front Genet 2019; 9:636. [PMID: 30723492 PMCID: PMC6349826 DOI: 10.3389/fgene.2018.00636] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/27/2018] [Indexed: 12/12/2022] Open
Abstract
Gene expression profiling is a useful tool to predict and interrogate mechanisms of toxicity. RNA-Seq technology has emerged as an attractive alternative to traditional microarray platforms for conducting transcriptional profiling. The objective of this work was to compare both transcriptomic platforms to determine whether RNA-Seq offered significant advantages over microarrays for toxicogenomic studies. RNA samples from the livers of rats treated for 5 days with five tool hepatotoxicants (α-naphthylisothiocyanate/ANIT, carbon tetrachloride/CCl4, methylenedianiline/MDA, acetaminophen/APAP, and diclofenac/DCLF) were analyzed with both gene expression platforms (RNA-Seq and microarray). Data were compared to determine any potential added scientific (i.e., better biological or toxicological insight) value offered by RNA-Seq compared to microarrays. RNA-Seq identified more differentially expressed protein-coding genes and provided a wider quantitative range of expression level changes when compared to microarrays. Both platforms identified a larger number of differentially expressed genes (DEGs) in livers of rats treated with ANIT, MDA, and CCl4 compared to APAP and DCLF, in agreement with the severity of histopathological findings. Approximately 78% of DEGs identified with microarrays overlapped with RNA-Seq data, with a Spearman’s correlation of 0.7 to 0.83. Consistent with the mechanisms of toxicity of ANIT, APAP, MDA and CCl4, both platforms identified dysregulation of liver relevant pathways such as Nrf2, cholesterol biosynthesis, eiF2, hepatic cholestasis, glutathione and LPS/IL-1 mediated RXR inhibition. RNA-Seq data showed additional DEGs that not only significantly enriched these pathways, but also suggested modulation of additional liver relevant pathways. In addition, RNA-Seq enabled the identification of non-coding DEGs that offer a potential for improved mechanistic clarity. Overall, these results indicate that RNA-Seq is an acceptable alternative platform to microarrays for rat toxicogenomic studies with several advantages. Because of its wider dynamic range as well as its ability to identify a larger number of DEGs, RNA-Seq may generate more insight into mechanisms of toxicity. However, more extensive reference data will be necessary to fully leverage these additional RNA-Seq data, especially for non-coding sequences.
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Affiliation(s)
- Mohan S Rao
- Investigative Toxicology and Pathology, Global Preclinical Safety, AbbVie, North Chicago, IL, United States
| | - Terry R Van Vleet
- Investigative Toxicology and Pathology, Global Preclinical Safety, AbbVie, North Chicago, IL, United States
| | - Rita Ciurlionis
- Investigative Toxicology and Pathology, Global Preclinical Safety, AbbVie, North Chicago, IL, United States
| | - Wayne R Buck
- Investigative Toxicology and Pathology, Global Preclinical Safety, AbbVie, North Chicago, IL, United States
| | - Scott W Mittelstadt
- Investigative Toxicology and Pathology, Global Preclinical Safety, AbbVie, North Chicago, IL, United States
| | - Eric A G Blomme
- Investigative Toxicology and Pathology, Global Preclinical Safety, AbbVie, North Chicago, IL, United States
| | - Michael J Liguori
- Investigative Toxicology and Pathology, Global Preclinical Safety, AbbVie, North Chicago, IL, United States
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Alexander-Dann B, Pruteanu LL, Oerton E, Sharma N, Berindan-Neagoe I, Módos D, Bender A. Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. Mol Omics 2018; 14:218-236. [PMID: 29917034 PMCID: PMC6080592 DOI: 10.1039/c8mo00042e] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/08/2018] [Indexed: 12/12/2022]
Abstract
The toxicogenomics field aims to understand and predict toxicity by using 'omics' data in order to study systems-level responses to compound treatments. In recent years there has been a rapid increase in publicly available toxicological and 'omics' data, particularly gene expression data, and a corresponding development of methods for its analysis. In this review, we summarize recent progress relating to the analysis of RNA-Seq and microarray data, review relevant databases, and highlight recent applications of toxicogenomics data for understanding and predicting compound toxicity. These include the analysis of differentially expressed genes and their enrichment, signature matching, methods based on interaction networks, and the analysis of co-expression networks. In the future, these state-of-the-art methods will likely be combined with new technologies, such as whole human body models, to produce a comprehensive systems-level understanding of toxicity that reduces the necessity of in vivo toxicity assessment in animal models.
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Affiliation(s)
- Benjamin Alexander-Dann
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Lavinia Lorena Pruteanu
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
- Babeş-Bolyai University
, Institute for Doctoral Studies
,
1 Kogălniceanu Street
, Cluj-Napoca 400084
, Romania
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, MedFuture Research Centre for Advanced Medicine
,
23 Marinescu Street/4-6 Pasteur Street
, Cluj-Napoca 400337
, Romania
| | - Erin Oerton
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Nitin Sharma
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Ioana Berindan-Neagoe
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, MedFuture Research Centre for Advanced Medicine
,
23 Marinescu Street/4-6 Pasteur Street
, Cluj-Napoca 400337
, Romania
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, Research Center for Functional Genomics
, Biomedicine and Translational Medicine
,
23 Marinescu Street
, Cluj-Napoca 400337
, Romania
- The Oncology Institute “Prof. Dr Ion Chiricuţă”
, Department of Functional Genomics and Experimental Pathology
,
34-36 Republicii Street
, Cluj-Napoca 400015
, Romania
| | - Dezső Módos
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Andreas Bender
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
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22
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Saladino F, Posarelli E, Luz C, Luciano F, Rodriguez-Estrada M, Mañes J, Meca G. Influence of probiotic microorganisms on aflatoxins B 1 and B 2 bioaccessibility evaluated with a simulated gastrointestinal digestion. J Food Compost Anal 2018. [DOI: 10.1016/j.jfca.2017.01.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Merrick BA, Chang JS, Phadke DP, Bostrom MA, Shah RR, Wang X, Gordon O, Wright GM. HAfTs are novel lncRNA transcripts from aflatoxin exposure. PLoS One 2018; 13:e0190992. [PMID: 29351317 PMCID: PMC5774710 DOI: 10.1371/journal.pone.0190992] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/22/2017] [Indexed: 12/28/2022] Open
Abstract
The transcriptome can reveal insights into precancer biology. We recently conducted RNA-Seq analysis on liver RNA from male rats exposed to the carcinogen, aflatoxin B1 (AFB1), for 90 days prior to liver tumor onset. Among >1,000 differentially expressed transcripts, several novel, unannotated Cufflinks-assembled transcripts, or HAfTs (Hepatic Aflatoxin Transcripts) were found. We hypothesized PCR-cloning and RACE (rapid amplification of cDNA ends) could further HAfT identification. Sanger data was obtained for 6 transcripts by PCR and 16 transcripts by 5’- and 3’-RACE. BLAST alignments showed, with two exceptions, HAfT transcripts were lncRNAs, >200nt without apparent long open reading frames. Six rat HAfT transcripts were classified as ‘novel’ without RefSeq annotation. Sequence alignment and genomic synteny showed each rat lncRNA had a homologous locus in the mouse genome and over half had homologous loci in the human genome, including at least two loci (and possibly three others) that were previously unannotated. While HAfT functions are not yet clear, coregulatory roles may be possible from their adjacent orientation to known coding genes with altered expression that include 8 HAfT-gene pairs. For example, a unique rat HAfT, homologous to Pvt1, was adjacent to known genes controlling cell proliferation. Additionally, PCR and RACE Sanger sequencing showed many alternative splice variants and refinements of exon sequences compared to Cufflinks assembled transcripts and gene prediction algorithms. Presence of multiple splice variants and short tandem repeats found in some HAfTs may be consequential for secondary structure, transcriptional regulation, and function. In summary, we report novel, differentially expressed lncRNAs after exposure to the genotoxicant, AFB1, prior to neoplastic lesions. Complete cloning and sequencing of such transcripts could pave the way for a new set of sensitive and early prediction markers for chemical hepatocarcinogens.
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Affiliation(s)
- B. Alex Merrick
- Biomolecular Screening Branch, Division National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
- * E-mail:
| | - Justin S. Chang
- Biomolecular Screening Branch, Division National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Dhiral P. Phadke
- Sciome, LLC, Research Triangle Park, North Carolina, United States of America
| | - Meredith A. Bostrom
- Genomics Laboratory, David H. Murdock Research Institute, Kannapolis, North Carolina, United State of America
| | - Ruchir R. Shah
- Sciome, LLC, Research Triangle Park, North Carolina, United States of America
| | - Xinguo Wang
- Genomics Laboratory, David H. Murdock Research Institute, Kannapolis, North Carolina, United State of America
| | - Oksana Gordon
- Genomics Laboratory, David H. Murdock Research Institute, Kannapolis, North Carolina, United State of America
| | - Garron M. Wright
- Genomics Laboratory, David H. Murdock Research Institute, Kannapolis, North Carolina, United State of America
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24
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Reed KM, Mendoza KM, Abrahante JE, Coulombe RA. Comparative Response of the Hepatic Transcriptomes of Domesticated and Wild Turkey to Aflatoxin B₁. Toxins (Basel) 2018; 10:toxins10010042. [PMID: 29342849 PMCID: PMC5793129 DOI: 10.3390/toxins10010042] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/15/2022] Open
Abstract
The food-borne mycotoxin aflatoxin B1 (AFB1) poses a significant risk to poultry, which are highly susceptible to its hepatotoxic effects. Domesticated turkeys (Meleagris gallopavo) are especially sensitive, whereas wild turkeys (M. g. silvestris) are more resistant. AFB1 toxicity entails bioactivation by hepatic cytochrome P450s to the electrophilic exo-AFB1-8,9-epoxide (AFBO). Domesticated turkeys lack functional hepatic GST-mediated detoxification of AFBO, and this is largely responsible for the differences in resistance between turkey types. This study was designed to characterize transcriptional changes induced in turkey livers by AFB1, and to contrast the response of domesticated (susceptible) and wild (more resistant) birds. Gene expression responses to AFB1 were examined using RNA-sequencing. Statistically significant differences in gene expression were observed among treatment groups and between turkey types. Expression analysis identified 4621 genes with significant differential expression (DE) in AFB1-treated birds compared to controls. Characterization of DE transcripts revealed genes dis-regulated in response to toxic insult with significant association of Phase I and Phase II genes and others important in cellular regulation, modulation of apoptosis, and inflammatory responses. Constitutive expression of GSTA3 was significantly higher in wild birds and was significantly higher in AFB1-treated birds when compared to controls for both genetic groups. This pattern was also observed by qRT-PCR in other wild and domesticated turkey strains. Results of this study emphasize the differential response of these genetically distinct birds, and identify genes and pathways that are differentially altered in aflatoxicosis.
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Affiliation(s)
- Kent M Reed
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA.
| | - Kristelle M Mendoza
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN 55108, USA.
| | - Juan E Abrahante
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Roger A Coulombe
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture, Utah State University, Logan, UT 84322, USA.
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25
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Souza TM, Rieswijk L, Beucken TVD, Kleinjans J, Jennen D. Persistent transcriptional responses show the involvement of feed-forward control in a repeated dose toxicity study. Toxicology 2016; 375:58-63. [PMID: 27765683 DOI: 10.1016/j.tox.2016.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 01/17/2023]
Abstract
Chemical carcinogenesis, albeit complex, often relies on modulation of transcription through activation or repression of key transcription factors. While analyzing extensive networks may hinder the biological interpretation, one may focus on dynamic network motifs, among which persistent feed-forward loops (FFLs) are known to chronically influence transcriptional programming. Here, to investigate the relevance a FFL-oriented approach in depth, we have focused on aflatoxin B1-induced transcriptomic alterations during distinct states of exposure (daily administration during 5days followed by a non-exposed period) of human hepatocytes, by exploring known interactions in human transcription. Several TF-coding genes were persistently deregulated after washout of AFB1. Oncogene MYC was identified as the prominent regulator and driver of many FFLs, among which a FFL comprising MYC/HIF1A was the most recurrent. The MYC/HIF1A FFL was also identified and validated in an independent set as the master regulator of metabolic alterations linked to initiation and progression of carcinogenesis, i.e. the Warburg effect, possibly as result of persistent intracellular alterations arising from AFB1 exposure (nuclear and mitochondrial DNA damage, oxidative stress, transcriptional activation by secondary messengers). In summary, our analysis shows the involvement of FFLs as modulators of gene expression suggestive of a carcinogenic potential even after termination of exposure.
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Affiliation(s)
- Terezinha M Souza
- Department of Toxicogenomics, Maastricht University, Maastricht, 6229 ER, The Netherlands.
| | - Linda Rieswijk
- Department of Toxicogenomics, Maastricht University, Maastricht, 6229 ER, The Netherlands.
| | - Twan van den Beucken
- Department of Toxicogenomics, Maastricht University, Maastricht, 6229 ER, The Netherlands.
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, 6229 ER, The Netherlands.
| | - Danyel Jennen
- Department of Toxicogenomics, Maastricht University, Maastricht, 6229 ER, The Netherlands.
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26
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Perilla Oil Supplementation Ameliorates High-Fat/High-Cholesterol Diet Induced Nonalcoholic Fatty Liver Disease in Rats via Enhanced Fecal Cholesterol and Bile Acid Excretion. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2384561. [PMID: 27642591 PMCID: PMC5013210 DOI: 10.1155/2016/2384561] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 07/31/2016] [Indexed: 02/06/2023]
Abstract
Recent experimental studies and clinical trials have shown that hepatic cholesterol metabolic disorders are closely related to the development of nonalcoholic fatty liver disease (NAFLD). The main goal of this study was to investigate the efficacy of the perilla oil rich in alpha-linolenic acid (ALA) against NASH and gain a deep insight into its potential mechanisms. Rats were fed a high-fat/high-cholesterol diet (HFD) supplement with perilla oil (POH) for 16 weeks. Routine blood biochemical tests and histological staining illustrated that the perilla oil administration improved HFD-induced hyperlipidemia, reduced hepatic steatosis, and inhibited hepatic inflammatory infiltration and fibrosis. Perilla oil also increased fecal bile acid and cholesterol excretion. Hepatic RNA-Seq analysis found that the long time perilla oil supplement notably modified the gene expression involved in cholesterol metabolism. Our results implicate that, after long-term high level dietary cholesterol feeding, rat liver endogenous synthesis of cholesterol and cholesterol-rich low density lipoprotein uptake was significantly inhibited, and perilla oil did not modulate expression of genes responsible for cholesterol synthesis but did increase cholesterol removed from hepatocytes by conversion to bile acids and increased fecal cholesterol excretion.
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27
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Shi J, He J, Lin J, Sun X, Sun F, Ou C, Jiang C. Distinct response of the hepatic transcriptome to Aflatoxin B1 induced hepatocellular carcinogenesis and resistance in rats. Sci Rep 2016; 6:31898. [PMID: 27545718 PMCID: PMC4992951 DOI: 10.1038/srep31898] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 07/28/2016] [Indexed: 11/26/2022] Open
Abstract
Aflatoxin is a natural potent carcinogen and a major cause of liver cancer. However, the molecular mechanisms of hepatocellular carcinogenesis remain largely unexplored. In this study, we profiled global gene expression in liver tissues of rats that developed hepatocellular carcinoma (HCC) from aflatoxin B1 (AFB1) administration and those that were AFB1-resistant, as well as rats without AFB1 exposure as a control. AFB1 exposure resulted in extensive perturbation in gene expression with different functions in HCC and AFB1 resistance (AR) samples. The differentially expressed genes (DEGs) in HCC sample were enriched for cell proliferation, cell adhesion and vasculature development that largely contribute to carcinogenesis. Anti-apoptosis genes were up-regulated in HCC sample whereas apoptosis-induction genes were up-regulated in AR sample. AFB1 exposure also caused extensive alteration in expression level of lncRNAs. Among all the 4511 annotated lncRNAs, half of them were highly expressed only in HCC sample and up-regulated a group of protein-coding genes with cancer-related functions: apoptosis regulation, DNA repair, and cell cycle. Intriguingly, these genes were down-regulated by lncRNAs highly expressed in AR sample. Collectively, apoptosis is the critical biological process for carcinogenesis in response to AFB1 exposure through changes in expression level of both protein-coding and lncRNA genes.
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Affiliation(s)
- Jiejun Shi
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China.,Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiangtu He
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China
| | - Jing Lin
- Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xin Sun
- Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Fenyong Sun
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China
| | - Chao Ou
- Department of Clinical Laboratory, the Affiliated Tumor Hospital of Guangxi Medical University, Nanning, Guangxi Province, China
| | - Cizhong Jiang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China.,Shanghai Key Laboratory of Signaling and Disease Research, the School of Life Sciences and Technology, Tongji University, Shanghai, China
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28
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Busche T, Winkler A, Wedderhoff I, Rückert C, Kalinowski J, Ortiz de Orué Lucana D. Deciphering the Transcriptional Response Mediated by the Redox-Sensing System HbpS-SenS-SenR from Streptomycetes. PLoS One 2016; 11:e0159873. [PMID: 27541358 PMCID: PMC4991794 DOI: 10.1371/journal.pone.0159873] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/08/2016] [Indexed: 12/30/2022] Open
Abstract
The secreted protein HbpS, the membrane-embedded sensor kinase SenS and the cytoplasmic response regulator SenR from streptomycetes have been shown to form a novel type of signaling pathway. Based on structural biology as well as different biochemical and biophysical approaches, redox stress-based post-translational modifications in the three proteins were shown to modulate the activity of this signaling pathway. In this study, we show that the homologous system, named here HbpSc-SenSc-SenRc, from the model species Streptomyces coelicolor A3(2) provides this bacterium with an efficient defense mechanism under conditions of oxidative stress. Comparative analyses of the transcriptomes of the Streptomyces coelicolor A3(2) wild-type and the generated hbpSc-senSc-senRc mutant under native and oxidative-stressing conditions allowed to identify differentially expressed genes, whose products may enhance the anti-oxidative defense of the bacterium. Amongst others, the results show an up-regulated transcription of genes for biosynthesis of cysteine and vitamin B12, transport of methionine and vitamin B12, and DNA synthesis and repair. Simultaneously, transcription of genes for degradation of an anti-oxidant compound is down-regulated in a HbpSc-SenSc-SenRc-dependent manner. It appears that HbpSc-SenSc-SenRc controls the non-enzymatic response of Streptomyces coelicolor A3(2) to counteract the hazardous effects of oxidative stress. Binding of the response regulator SenRc to regulatory regions of some of the studied genes indicates that the regulation is direct. The results additionally suggest that HbpSc-SenSc-SenRc may act in concert with other regulatory modules such as a transcriptional regulator, a two-component system and the Streptomyces B12 riboswitch. The transcriptomics data, together with our previous in vitro results, enable a profound characterization of the HbpS-SenS-SenR system from streptomycetes. Since homologues to HbpS-SenS-SenR are widespread in different actinobacteria with ecological and medical relevance, the data presented here will serve as a basis to elucidate the biological role of these homologues.
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Affiliation(s)
- Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Anika Winkler
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Ina Wedderhoff
- Applied Genetics of Microorganisms, Department of Biology and Chemistry, University of Osnabrueck, Osnabrueck, Barbarastraße 13, 49076, Osnabrueck, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany
| | - Darío Ortiz de Orué Lucana
- Applied Genetics of Microorganisms, Department of Biology and Chemistry, University of Osnabrueck, Osnabrueck, Barbarastraße 13, 49076, Osnabrueck, Germany
- * E-mail:
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29
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Monestier O, Blanquet V. WFIKKN1 and WFIKKN2: "Companion" proteins regulating TGFB activity. Cytokine Growth Factor Rev 2016; 32:75-84. [PMID: 27325460 DOI: 10.1016/j.cytogfr.2016.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/07/2016] [Accepted: 06/10/2016] [Indexed: 01/14/2023]
Abstract
The WFIKKN (WAP, Follistatin/kazal, Immunoglobulin, Kunitz and Netrin domain-containing) protein family is composed of two multidomain proteins: WFIKKN1 and WFIKKN2. They were formed by domain shuffling and are likely present in deuterostoms. The WFIKKN (also called GASP) proteins are well known for their function in muscle and skeletal tissues, namely, inhibition of certain members of the transforming growth factor beta (TGFB) superfamily such as myostatin (MSTN) and growth and differentiation factor 11 (GDF11). However, the role of the WFIKKN proteins in other tissues is still poorly understood in spite of evidence suggesting possible action in the inner ear, brain and reproduction. Further, several recent studies based on next generation technologies revealed differential expression of WFIKKN1 and WFIKKN2 in various tissues suggesting that their function is not limited to MSTN and GDF11 inhibition in musculoskeletal tissue. In this review, we summarize current knowledge about the WFIKKN proteins and propose that they are "companion" proteins for various growth factors by providing localized and sustained presentation of TGFB proteins to their respective receptors, thus regulating the balance between the activation of Smad and non-Smad pathways by TGFB.
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Affiliation(s)
- Olivier Monestier
- INRA, UR1037 Laboratory of Fish Physiology and Genomic, Growth and Flesh Quality Group, Campus de Beaulieu, 35000 Rennes, France.
| | - Véronique Blanquet
- INRA, UMR1061 Unité de Génétique Moléculaire Animale, 87060 Limoges, France; Université de Limoges, 87060 Limoges, France.
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30
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Dunnick JK, Merrick BA, Brix A, Morgan DL, Gerrish K, Wang Y, Flake G, Foley J, Shockley KR. Molecular Changes in the Nasal Cavity after N, N-dimethyl-p-toluidine Exposure. Toxicol Pathol 2016; 44:835-47. [PMID: 27099258 DOI: 10.1177/0192623316637708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
N, N-dimethyl-p-toluidine (DMPT; Cas No. 99-97-8), an accelerant for methyl methacrylate monomers in medical devices, is a nasal cavity carcinogen according to a 2-yr cancer study of male and female F344/N rats, with the nasal tumors arising from the transitional cell epithelium. In this study, we exposed male F344/N rats for 5 days to DMPT (0, 1, 6, 20, 60, or 120 mg/kg [oral gavage]) to explore the early changes in the nasal cavity after short-term exposure. Lesions occurred in the nasal cavity including hyperplasia of transitional cell epithelium (60 and 120 mg/kg). Nasal tissue was rapidly removed and preserved for subsequent laser capture microdissection and isolation of the transitional cell epithelium (0 and 120 mg/kg) for transcriptomic studies. DMPT transitional cell epithelium gene transcript patterns were characteristic of an antioxidative damage response (e.g., Akr7a3, Maff, and Mgst3), cell proliferation, and decrease in signals for apoptosis. The transcripts of amino acid transporters were upregulated (e.g., Slc7a11). The DMPT nasal transcript expression pattern was similar to that found in the rat nasal cavity after formaldehyde exposure, with over 1,000 transcripts in common. Molecular changes in the nasal cavity after DMPT exposure suggest that oxidative damage is a mechanism of the DMPT toxic and/or carcinogenic effects.
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Affiliation(s)
- June K Dunnick
- Toxicology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - B Alex Merrick
- Biomolecular Screening Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Amy Brix
- Experimental Pathology Laboratories, Inc., Research Triangle Park, North Carolina, USA
| | - Daniel L Morgan
- NTP Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Kevin Gerrish
- Molecular Genomics Core, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Yu Wang
- Cellular and Molecular Pathology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Gordon Flake
- Cellular and Molecular Pathology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Julie Foley
- Cellular and Molecular Pathology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Keith R Shockley
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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31
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Li J, Bushel PR. EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data. BMC Genomics 2016; 17:255. [PMID: 27004791 PMCID: PMC4804494 DOI: 10.1186/s12864-016-2584-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/11/2016] [Indexed: 11/29/2022] Open
Abstract
Background RNA sequencing (RNA-Seq) measures genome-wide gene expression. RNA-Seq data is count-based rendering normal distribution models for analysis inappropriate. Normalization of RNA-Seq data to transform the data has limitations which can adversely impact the analysis. Furthermore, there are a few count-based methods for analysis of RNA-Seq data but they are essentially for pairwise analysis of treatment groups or multiclasses but not pattern-based to identify co-expressed genes. Results We adapted our extracting patterns and identifying genes methodology for RNA-Seq (EPIG-Seq) count data. The software uses count-based correlation to measure similarity between genes, quasi-Poisson modelling to estimate dispersion in the data and a location parameter to indicate magnitude of differential expression. EPIG-Seq is different than any other software currently available for pattern analysis of RNA-Seq data in that EPIG-Seq 1) uses count level data and supports cases of inflated zeros, 2) identifies statistically significant clusters of genes that are co-expressed across experimental conditions, 3) takes into account dispersion in the replicate data and 4) provides reliable results even with small sample sizes. EPIG-Seq operates in two steps: 1) extract the pattern profiles from data as seeds for clustering co-expressed genes and 2) cluster the genes to the pattern seeds and compute statistical significance of the pattern of co-expressed genes. EPIG-Seq provides a table of the genes with bootstrapped p-values and profile plots of the patterns of co-expressed genes. In addition, EPIG-Seq provides a heat map and principal component dimension reduction plot of the clustered genes as visual aids. We demonstrate the utility of EPIG-Seq through the analysis of toxicogenomics and cancer data sets to identify biologically relevant co-expressed genes. EPIG-Seq is available at: sourceforge.net/projects/epig-seq. Conclusions EPIG-Seq is unlike any other software currently available for pattern analysis of RNA-Seq count level data across experimental groups. Using the EPIG-Seq software to analyze RNA-Seq count data across biological conditions permits the ability to extract biologically meaningful co-expressed genes associated with coordinated regulation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2584-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jianying Li
- Integrative Bioinformatics Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.,Microarray and Genome Informatics Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.,Kelly Government Solutions, Research Triangle Park, NC, 27709, USA
| | - Pierre R Bushel
- Microarray and Genome Informatics Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA. .,Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC, 27709, USA.
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Lamontagne J, Mell JC, Bouchard MJ. Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression. PLoS Pathog 2016; 12:e1005438. [PMID: 26891448 PMCID: PMC4758756 DOI: 10.1371/journal.ppat.1005438] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 01/13/2016] [Indexed: 12/11/2022] Open
Abstract
Globally, a chronic hepatitis B virus (HBV) infection remains the leading cause of primary liver cancer. The mechanisms leading to the development of HBV-associated liver cancer remain incompletely understood. In part, this is because studies have been limited by the lack of effective model systems that are both readily available and mimic the cellular environment of a normal hepatocyte. Additionally, many studies have focused on single, specific factors or pathways that may be affected by HBV, without addressing cell physiology as a whole. Here, we apply RNA-seq technology to investigate transcriptome-wide, HBV-mediated changes in gene expression to identify single factors and pathways as well as networks of genes and pathways that are affected in the context of HBV replication. Importantly, these studies were conducted in an ex vivo model of cultured primary hepatocytes, allowing for the transcriptomic characterization of this model system and an investigation of early HBV-mediated effects in a biologically relevant context. We analyzed differential gene expression within the context of time-mediated gene-expression changes and show that in the context of HBV replication a number of genes and cellular pathways are altered, including those associated with metabolism, cell cycle regulation, and lipid biosynthesis. Multiple analysis pipelines, as well as qRT-PCR and an independent, replicate RNA-seq analysis, were used to identify and confirm differentially expressed genes. HBV-mediated alterations to the transcriptome that we identified likely represent early changes to hepatocytes following an HBV infection, suggesting potential targets for early therapeutic intervention. Overall, these studies have produced a valuable resource that can be used to expand our understanding of the complex network of host-virus interactions and the impact of HBV-mediated changes to normal hepatocyte physiology on viral replication. Chronic infection with the hepatitis B virus (HBV) is the leading global cause of primary liver cancer; however, therapeutics for the treatment of chronic HBV are limited in both scope and efficacy. Infection with HBV results in an incompletely understood, complex network of host-virus interactions. To attempt to better understand these interactions, we assessed HBV-mediated changes to normal hepatocyte gene expression on a transcriptome-wide scale. By identifying gene expression that is altered by HBV, we were able to demonstrate that HBV affects multiple cellular signaling pathways that previously have been associated with carcinogenesis. As most HBV-related studies have investigated either late-stage changes in hepatocyte physiology or looked at cellular changes on a more narrow scale, our results represent an important advancement towards identifying early events associated with HBV replication, upstream of the development of HBV-associated disease. Additionally, our studies allowed us to characterize transcriptome changes that occur in a primary hepatocyte culture model, an important advancement in the confirmation of this commonly used model system as a biologically relevant alternative to transformed cell lines.
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Affiliation(s)
- Jason Lamontagne
- Graduate Program in Microbiology and Immunology, Graduate School of Biomedical Sciences and Professional Studies, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Joshua C. Mell
- Department of Microbiology and Immunology, Center for Genomic Sciences, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Michael J. Bouchard
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Hu Y, Xie S, Yao J. Identification of Novel Reference Genes Suitable for qRT-PCR Normalization with Respect to the Zebrafish Developmental Stage. PLoS One 2016; 11:e0149277. [PMID: 26891128 PMCID: PMC4758726 DOI: 10.1371/journal.pone.0149277] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/29/2016] [Indexed: 12/20/2022] Open
Abstract
Reference genes used in normalizing qRT-PCR data are critical for the accuracy of gene expression analysis. However, many traditional reference genes used in zebrafish early development are not appropriate because of their variable expression levels during embryogenesis. In the present study, we used our previous RNA-Seq dataset to identify novel reference genes suitable for gene expression analysis during zebrafish early developmental stages. We first selected 197 most stably expressed genes from an RNA-Seq dataset (29,291 genes in total), according to the ratio of their maximum to minimum RPKM values. Among the 197 genes, 4 genes with moderate expression levels and the least variation throughout 9 developmental stages were identified as candidate reference genes. Using four independent statistical algorithms (delta-CT, geNorm, BestKeeper and NormFinder), the stability of qRT-PCR expression of these candidates was then evaluated and compared to that of actb1 and actb2, two commonly used zebrafish reference genes. Stability rankings showed that two genes, namely mobk13 (mob4) and lsm12b, were more stable than actb1 and actb2 in most cases. To further test the suitability of mobk13 and lsm12b as novel reference genes, they were used to normalize three well-studied target genes. The results showed that mobk13 and lsm12b were more suitable than actb1 and actb2 with respect to zebrafish early development. We recommend mobk13 and lsm12b as new optimal reference genes for zebrafish qRT-PCR analysis during embryogenesis and early larval stages.
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Affiliation(s)
- Yu Hu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuying Xie
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jihua Yao
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
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Zhang X, Li CR, Wang WC, Xue J, Huang YL, Yang XX, Tan B, Zhou XP, Shao C, Ding SJ, Qiu JF. A novel electrochemical immunosensor for highly sensitive detection of aflatoxin B1 in corn using single-walled carbon nanotubes/chitosan. Food Chem 2016; 192:197-202. [DOI: 10.1016/j.foodchem.2015.06.044] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 11/19/2014] [Accepted: 06/16/2015] [Indexed: 10/23/2022]
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Monson MS, Cardona CJ, Coulombe RA, Reed KM. Hepatic Transcriptome Responses of Domesticated and Wild Turkey Embryos to Aflatoxin B₁. Toxins (Basel) 2016; 8:toxins8010016. [PMID: 26751476 PMCID: PMC4728538 DOI: 10.3390/toxins8010016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 12/23/2015] [Accepted: 12/30/2015] [Indexed: 11/16/2022] Open
Abstract
The mycotoxin, aflatoxin B₁ (AFB₁) is a hepatotoxic, immunotoxic, and mutagenic contaminant of food and animal feeds. In poultry, AFB₁ can be maternally transferred to embryonated eggs, affecting development, viability and performance after hatch. Domesticated turkeys (Meleagris gallopavo) are especially sensitive to aflatoxicosis, while Eastern wild turkeys (M. g. silvestris) are likely more resistant. In ovo exposure provided a controlled AFB₁ challenge and comparison of domesticated and wild turkeys. Gene expression responses to AFB₁ in the embryonic hepatic transcriptome were examined using RNA-sequencing (RNA-seq). Eggs were injected with AFB₁ (1 μg) or sham control and dissected for liver tissue after 1 day or 5 days of exposure. Libraries from domesticated turkey (n = 24) and wild turkey (n = 15) produced 89.2 Gb of sequence. Approximately 670 M reads were mapped to a turkey gene set. Differential expression analysis identified 1535 significant genes with |log₂ fold change| ≥ 1.0 in at least one pair-wise comparison. AFB₁ effects were dependent on exposure time and turkey type, occurred more rapidly in domesticated turkeys, and led to notable up-regulation in cell cycle regulators, NRF2-mediated response genes and coagulation factors. Further investigation of NRF2-response genes may identify targets to improve poultry resistance.
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Affiliation(s)
- Melissa S Monson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA.
| | - Carol J Cardona
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA.
| | - Roger A Coulombe
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture, Utah State University, Logan, UT 84322, USA.
| | - Kent M Reed
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA.
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Accardi R, Gruffat H, Sirand C, Fusil F, Gheit T, Hernandez-Vargas H, Le Calvez-Kelm F, Traverse-Glehen A, Cosset FL, Manet E, Wild CP, Tommasino M. The mycotoxin aflatoxin B1 stimulates Epstein-Barr virus-induced B-cell transformation in in vitro and in vivo experimental models. Carcinogenesis 2015; 36:1440-51. [PMID: 26424750 DOI: 10.1093/carcin/bgv142] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/20/2015] [Indexed: 01/09/2023] Open
Abstract
Although Epstein-Barr virus (EBV) infection is widely distributed, certain EBV-driven malignancies are geographically restricted. EBV-associated Burkitt's lymphoma (eBL) is endemic in children living in sub-Saharan Africa. This population is heavily exposed to food contaminated with the mycotoxin aflatoxin B1 (AFB1). Here, we show that exposure to AFB1 in in vitro and in vivo models induces activation of the EBV lytic cycle and increases EBV load, two events that are associated with an increased risk of eBL in vivo. AFB1 treatment leads to the alteration of cellular gene expression, with consequent activations of signaling pathways, e.g. PI3K, that in turn mediate reactivation of the EBV life cycle. Finally, we show that AFB1 triggers EBV-driven cellular transformation both in primary human B cells and in a humanized animal model. In summary, our data provide evidence for a role of AFB1 as a cofactor in EBV-mediated carcinogenesis.
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Affiliation(s)
- Rosita Accardi
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon 69372, France,
| | - Henri Gruffat
- EVIR and Oncogenic Herpesviruses Teams, International Center for Infectiology Research, Université de Lyon, Lyon 69007, France, INSERM, U1111, Lyon 69007, France, Human Virology, Ecole Normale Supérieure de Lyon, Lyon 69007, France, Centre International de Recherche en Infectiologie, Université Lyon 1, Lyon 69007, France and
| | - Cécilia Sirand
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon 69372, France
| | - Floriane Fusil
- EVIR and Oncogenic Herpesviruses Teams, International Center for Infectiology Research, Université de Lyon, Lyon 69007, France, INSERM, U1111, Lyon 69007, France, Human Virology, Ecole Normale Supérieure de Lyon, Lyon 69007, France, Centre International de Recherche en Infectiologie, Université Lyon 1, Lyon 69007, France and
| | - Tarik Gheit
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon 69372, France
| | - Hector Hernandez-Vargas
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon 69372, France
| | - Florence Le Calvez-Kelm
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon 69372, France
| | | | - François-Loïc Cosset
- EVIR and Oncogenic Herpesviruses Teams, International Center for Infectiology Research, Université de Lyon, Lyon 69007, France, INSERM, U1111, Lyon 69007, France, Human Virology, Ecole Normale Supérieure de Lyon, Lyon 69007, France, Centre International de Recherche en Infectiologie, Université Lyon 1, Lyon 69007, France and
| | - Evelyne Manet
- EVIR and Oncogenic Herpesviruses Teams, International Center for Infectiology Research, Université de Lyon, Lyon 69007, France, INSERM, U1111, Lyon 69007, France, Human Virology, Ecole Normale Supérieure de Lyon, Lyon 69007, France, Centre International de Recherche en Infectiologie, Université Lyon 1, Lyon 69007, France and
| | - Christopher P Wild
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon 69372, France
| | - Massimo Tommasino
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon 69372, France
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Wang W, Wang X, Zhang Y, Li Z, Xie X, Wang J, Gao M, Zhang S, Hou Y. Transcriptome Analysis of Canine Cardiac Fat Pads: Involvement of Two Novel Long Non-Coding RNAs in Atrial Fibrillation Neural Remodeling. J Cell Biochem 2015; 116:809-21. [PMID: 25559442 DOI: 10.1002/jcb.25037] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 12/11/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Weizong Wang
- Department of Cardiology; Shandong Provincial Qianfoshan Hospital; Shandong University; Jinan 250014 China
| | - Ximin Wang
- Department of Cardiology; Shandong Provincial Qianfoshan Hospital; Shandong University; Jinan 250014 China
| | - Yujiao Zhang
- Department of Cardiology; Shandong Provincial Qianfoshan Hospital; Shandong University; Jinan 250014 China
| | - Zhan Li
- Department of Cardiology; Shandong Provincial Qianfoshan Hospital; Shandong University; Jinan 250014 China
| | - Xinxing Xie
- Department of Cardiology; Shandong Provincial Qianfoshan Hospital; Shandong University; Jinan 250014 China
| | - Jiangrong Wang
- Department of Cardiology; Shandong Provincial Qianfoshan Hospital; Shandong University; Jinan 250014 China
| | - Mei Gao
- Department of Cardiology; Shandong Provincial Qianfoshan Hospital; Shandong University; Jinan 250014 China
| | - Shuyu Zhang
- School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions; Soochow University; Suzhou 215123 China
| | - Yinglong Hou
- Department of Cardiology; Shandong Provincial Qianfoshan Hospital; Shandong University; Jinan 250014 China
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Abstract
Systems biology and synthetic biology are emerging disciplines which are becoming increasingly utilised in several areas of bioscience. Toxicology is beginning to benefit from systems biology and we suggest in the future that is will also benefit from synthetic biology. Thus, a new era is on the horizon. This review illustrates how a suite of innovative techniques and tools can be applied to understanding complex health and toxicology issues. We review limitations confronted by the traditional computational approaches to toxicology and epidemiology research, using polycyclic aromatic hydrocarbons (PAHs) and their effects on adverse birth outcomes as an illustrative example. We introduce how systems toxicology (and their subdisciplines, genomic, proteomic, and metabolomic toxicology) will help to overcome such limitations. In particular, we discuss the advantages and disadvantages of mathematical frameworks that computationally represent biological systems. Finally, we discuss the nascent discipline of synthetic biology and highlight relevant toxicological centred applications of this technique, including improvements in personalised medicine. We conclude this review by presenting a number of opportunities and challenges that could shape the future of these rapidly evolving disciplines.
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Merrick BA, Paules RS, Tice RR. Intersection of toxicogenomics and high throughput screening in the Tox21 program: an NIEHS perspective. ACTA ACUST UNITED AC 2015; 14:7-27. [PMID: 27122658 DOI: 10.1504/ijbt.2015.074797] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Humans are exposed to thousands of chemicals with inadequate toxicological data. Advances in computational toxicology, robotic high throughput screening (HTS), and genome-wide expression have been integrated into the Tox21 program to better predict the toxicological effects of chemicals. Tox21 is a collaboration among US government agencies initiated in 2008 that aims to shift chemical hazard assessment from traditional animal toxicology to target-specific, mechanism-based, biological observations using in vitro assays and lower organism models. HTS uses biocomputational methods for probing thousands of chemicals in in vitro assays for gene-pathway response patterns predictive of adverse human health outcomes. In 1999, NIEHS began exploring the application of toxicogenomics to toxicology and recent advances in NextGen sequencing should greatly enhance the biological content obtained from HTS platforms. We foresee an intersection of new technologies in toxicogenomics and HTS as an innovative development in Tox21. Tox21 goals, priorities, progress, and challenges will be reviewed.
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Affiliation(s)
- B Alex Merrick
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Richard S Paules
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Raymond R Tice
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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40
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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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41
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Wang C, Gong B, Bushel PR, Thierry-Mieg J, Thierry-Mieg D, Xu J, Fang H, Hong H, Shen J, Su Z, Meehan J, Li X, Yang L, Li H, Łabaj PP, Kreil DP, Megherbi D, Florian C, Gaj S, van Delft J, Kleinjans J, Scherer A, Viswanath D, Wang J, Yang Y, Qian HR, Lancashire LJ, Bessarabova M, Nikolsky Y, Furlanello C, Chierici M, Albanese D, Jurman G, Riccadonna S, Filosi M, Visintainer R, Zhang KK, Li J, Hsieh JH, Svoboda DL, Fuscoe JC, Deng Y, Shi L, Paules RS, Auerbach SS, Tong W. The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nat Biotechnol 2014; 32:926-32. [PMID: 25150839 PMCID: PMC4243706 DOI: 10.1038/nbt.3001] [Citation(s) in RCA: 339] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 07/29/2014] [Indexed: 12/22/2022]
Abstract
The concordance of RNA-sequencing (RNA-seq) with microarrays for genome-wide analysis of differential gene expression has not been rigorously assessed using a range of chemical treatment conditions. Here we use a comprehensive study design to generate Illumina RNA-seq and Affymetrix microarray data from the same liver samples of rats exposed in triplicate to varying degrees of perturbation by 27 chemicals representing multiple modes of action (MOAs). The cross-platform concordance in terms of differentially expressed genes (DEGs) or enriched pathways is linearly correlated with treatment effect size (R(2)0.8). Furthermore, the concordance is also affected by transcript abundance and biological complexity of the MOA. RNA-seq outperforms microarray (93% versus 75%) in DEG verification as assessed by quantitative PCR, with the gain mainly due to its improved accuracy for low-abundance transcripts. Nonetheless, classifiers to predict MOAs perform similarly when developed using data from either platform. Therefore, the endpoint studied and its biological complexity, transcript abundance and the genomic application are important factors in transcriptomic research and for clinical and regulatory decision making.
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Affiliation(s)
- Charles Wang
- Center for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, USA
| | - Binsheng Gong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
| | - Pierre R. Bushel
- Microarray and Genome Informatics Group, National Institute of Environmental Health Sciences, RTP, North Carolina, USA
- Biostatistics Branch, National Institute of Environmental Health Sciences, RTP, North Carolina, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
| | - Hong Fang
- The Office of Scientific Coordination, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
| | - Jie Shen
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
| | - Zhenqiang Su
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
| | - Joe Meehan
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
| | - Xiaojin Li
- Functional Genomics Core, Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Lu Yang
- Functional Genomics Core, Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, California, USA
| | - Haiqing Li
- Functional Genomics Core, Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, California, USA
| | | | - David P. Kreil
- Boku University Vienna, Austria
- Life Sciences, University of Warwick, Coventry, U.K
| | - Dalila Megherbi
- CMINDS Research Center, Department of Electrical and Computer Engineering, Francis College of Engineering, University of Massachusetts, Lowell, Massachusetts, USA
| | - Caiment Florian
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Stan Gaj
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Joost van Delft
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Jos Kleinjans
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Andreas Scherer
- Australian Genome Research Facility Ltd, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | | | - Jian Wang
- Research Informatics and Statistics, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, USA
| | - Yong Yang
- Research Informatics and Statistics, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, USA
| | - Hui-Rong Qian
- Research Informatics and Statistics, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana, USA
| | | | | | - Yuri Nikolsky
- Thomson Reuters, IP & Science, Carlsbad, California, USA
| | | | | | | | | | | | | | | | - Ke K. Zhang
- Bioinformatics core, Department of Pathology, University of North Dakota, Grand Forks, North Dakota, USA
| | - Jianying Li
- Microarray and Genome Informatics Group, National Institute of Environmental Health Sciences, RTP, North Carolina, USA
- Kelly Government Solutions, Inc., Durham, North Carolina, USA
| | - Jui-Hua Hsieh
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, RTP, North Carolina, USA
| | | | - James C. Fuscoe
- Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
| | - Youping Deng
- Department of Internal Medicine and Biochemistry, Rush University Medical Center, Chicago, Illinois, USA
| | - Leming Shi
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
- Center for Pharmacogenomics, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai, China
| | - Richard S. Paules
- Laboratory of Toxicology and Pharmacology, National Institute of Environmental Health Sciences, RTP, North Carolina, USA
| | - Scott S. Auerbach
- Biomolecular Screening Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, RTP, North Carolina, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
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Zhang ZH, Jhaveri DJ, Marshall VM, Bauer DC, Edson J, Narayanan RK, Robinson GJ, Lundberg AE, Bartlett PF, Wray NR, Zhao QY. A comparative study of techniques for differential expression analysis on RNA-Seq data. PLoS One 2014; 9:e103207. [PMID: 25119138 PMCID: PMC4132098 DOI: 10.1371/journal.pone.0103207] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 06/30/2014] [Indexed: 01/23/2023] Open
Abstract
Recent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies, in particular for detecting differentially expressed genes between groups. Many software packages have been developed for the identification of differentially expressed genes (DEGs) between treatment groups based on RNA-Seq data. However, there is a lack of consensus on how to approach an optimal study design and choice of suitable software for the analysis. In this comparative study we evaluate the performance of three of the most frequently used software tools: Cufflinks-Cuffdiff2, DESeq and edgeR. A number of important parameters of RNA-Seq technology were taken into consideration, including the number of replicates, sequencing depth, and balanced vs. unbalanced sequencing depth within and between groups. We benchmarked results relative to sets of DEGs identified through either quantitative RT-PCR or microarray. We observed that edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives. Overall, DESeq or taking the intersection of DEGs from two or more tools is recommended if the number of false positives is a major concern in the study. In other circumstances, edgeR is slightly preferable for differential expression analysis at the expense of potentially introducing more false positives.
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Affiliation(s)
- Zong Hong Zhang
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Dhanisha J. Jhaveri
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Vikki M. Marshall
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Denis C. Bauer
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
- CSIRO Preventative Health Flagship and CSIRO Computational Informatics, Sydney, New South Wales, Australia
| | - Janette Edson
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
- The University of Queensland, Diamantina Institute, Brisbane, Queensland, Australia
| | - Ramesh K. Narayanan
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Gregory J. Robinson
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Andreas E. Lundberg
- Swedish University of Agricultural Sciences, Department of Clinical Sciences, Uppsala, Sweden
| | - Perry F. Bartlett
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Naomi R. Wray
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
| | - Qiong-Yi Zhao
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland, Australia
- * E-mail:
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43
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Mehrzad J, Devriendt B, Baert K, Cox E. Aflatoxin B1 interferes with the antigen-presenting capacity of porcine dendritic cells. Toxicol In Vitro 2014; 28:531-7. [DOI: 10.1016/j.tiv.2013.11.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 11/06/2013] [Accepted: 11/20/2013] [Indexed: 12/21/2022]
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Li G, Yi S, Yang F, Zhou Y, Ji Q, Cai J, Mei Y. Identification of mutant genes with high-frequency, high-risk, and high-expression in lung adenocarcinoma. Thorac Cancer 2014; 5:211-8. [PMID: 26767003 DOI: 10.1111/1759-7714.12080] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/28/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND To identify mutant genes with high-frequency-risk-expression between lung adenocarcinoma and normal samples. METHODS The ribonucleic acid RNA-Seq data GSE34914 and GSE37765 were downloaded from the Gene Expression Omnibus database, including 12 lung adenocarcinoma samples and six controls. All RNA-Seq reads were processed and the gene-expression level was calculated. Single nucleotide variation (SNV) was analyzed and the locations of mutant sites were recorded. In addition, the frequency and risk-level of mutant genes were calculated. Gene Ontology (GO) functional analysis was performed. The reported cancer genes were searched in tumor suppressor genes, Cancer Genes, and the Catalogue of Somatic Mutations in Cancer (COSMIC) database. RESULTS The SNV annotations of somatic mutation sites showed that 70% of mutation sites in the exon region occurred in the coding sequence (CDS). Thyroid hormone receptor interactor (TRIP)12 was identified with the highest frequency. A total of 118 mutant genes with high frequency and high-risk were selected and significantly enriched into several GO terms. No base mutation of cyclin C (CCNC) or RAB11A was recorded. At fragments per kilobase per million reads (FPKM) ≥ 56.5, reported tumor suppressor genes catenin (cadherin-associated protein), delta (CTNND)1, dual specificity phosphatase (DUSP)6, malate dehydrogenase (MDH)1 and RNA binding motif protein (RBM)5, were identified. Notably, signal transducer and activator of transcription 2 (STAT2) was the only transcription factor (TF) with high-risk mutation and its expression was detected. CONCLUSION For the mutant genes with high-frequency-risk-expression, CTNND1, DUSP6, MDH1 and RBM5 were identified. TRIP12 might be a potential cancer-related gene, and expression of TF STAT2 with high-risk was detected. These mutant gene candidates might promote the development of lung adenocarcinoma and provide new diagnostic potential targets for treatment.
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Affiliation(s)
- Guiyuan Li
- Department of Oncology, Tongji Hospital, Tongji University School of Medicine Shanghai, China
| | - Shengming Yi
- Department of Oncology, Tongji Hospital, Tongji University School of Medicine Shanghai, China
| | - Fan Yang
- Department of Clinical Laboratory Medicine, Tongji Hospital, Tongji University School of Medicine Shanghai, China
| | - Yongxin Zhou
- Department of Thoracic Cardiovascular Surgery, Tongji Hospital, Tongji University School of Medicine Shanghai, China
| | - Qiang Ji
- Department of Thoracic Cardiovascular Surgery, Tongji Hospital, Tongji University School of Medicine Shanghai, China
| | - Jianzhi Cai
- Department of Thoracic Cardiovascular Surgery, Tongji Hospital, Tongji University School of Medicine Shanghai, China
| | - Yunqing Mei
- Department of Thoracic Cardiovascular Surgery, Tongji Hospital, Tongji University School of Medicine Shanghai, China
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Johnson NM, Egner PA, Baxter VK, Sporn MB, Wible RS, Sutter TR, Groopman JD, Kensler TW, Roebuck BD. Complete protection against aflatoxin B(1)-induced liver cancer with a triterpenoid: DNA adduct dosimetry, molecular signature, and genotoxicity threshold. Cancer Prev Res (Phila) 2014; 7:658-65. [PMID: 24662598 DOI: 10.1158/1940-6207.capr-13-0430] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In experimental animals and humans, aflatoxin B1 (AFB1) is a potent hepatic toxin and carcinogen. The synthetic oleanane triterpenoid 1-[2-cyano-3-,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole (CDDO-Im), a powerful activator of Keap1-Nrf2 signaling, protects against AFB1-induced toxicity and preneoplastic lesion formation (GST-P-positive foci). This study assessed and mechanistically characterized the chemoprotective efficacy of CDDO-Im against AFB1-induced hepatocellular carcinoma (HCC). A lifetime cancer bioassay was undertaken in F344 rats dosed with AFB1 (200 μg/kg rat/day) for four weeks and receiving either vehicle or CDDO-Im (three times weekly), one week before and throughout the exposure period. Weekly, 24-hour urine samples were collected for analysis of AFB1 metabolites. In a subset of rats, livers were analyzed for GST-P foci. The comparative response of a toxicogenomic RNA expression signature for AFB1 was examined. CDDO-Im completely protected (0/20) against AFB1-induced liver cancer compared with a 96% incidence (22/23) observed in the AFB1 group. With CDDO-Im treatment, integrated level of urinary AFB1-N(7)-guanine was significantly reduced (66%) and aflatoxin-N-acetylcysteine, a detoxication product, was consistently elevated (300%) after the first AFB1 dose. In AFB1-treated rats, the hepatic burden of GST-P-positive foci increased substantially (0%-13.8%) over the four weeks, but was largely absent with CDDO-Im intervention. The toxicogenomic RNA expression signature characteristic of AFB1 was absent in the AFB1 + CDDO-Im-treated rats. The remarkable efficacy of CDDO-Im as an anticarcinogen is established even in the face of a significant aflatoxin adduct burden. Consequently, the absence of cancer requires a concept of a threshold for DNA damage for cancer development.
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Affiliation(s)
- Natalie M Johnson
- Authors' Affiliations: Department of Environmental Health Sciences, Bloomberg School of Public Health
| | - Patricia A Egner
- Authors' Affiliations: Department of Environmental Health Sciences, Bloomberg School of Public Health
| | - Victoria K Baxter
- Department of Molecular and Comparative Pathobiology, School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Michael B Sporn
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Ryan S Wible
- W. Harry Feinstone Center for Genomic Research, University of Memphis, Memphis, Tennessee; and
| | - Thomas R Sutter
- W. Harry Feinstone Center for Genomic Research, University of Memphis, Memphis, Tennessee; and
| | - John D Groopman
- Authors' Affiliations: Department of Environmental Health Sciences, Bloomberg School of Public Health
| | - Thomas W Kensler
- Authors' Affiliations: Department of Environmental Health Sciences, Bloomberg School of Public Health; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Bill D Roebuck
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Hanover, New Hampshire;
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Mohammadi A, Mehrzad J, Mahmoudi M, Schneider M. Environmentally Relevant Level of Aflatoxin B1 Dysregulates Human Dendritic Cells Through Signaling on Key Toll-Like Receptors. Int J Toxicol 2014; 33:175-186. [DOI: 10.1177/1091581814526890] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Aflatoxins (AFs) are highly hazardous fungal biometabolites usually present in feeds and foods. Aflatoxin B1 (AFB1) is the most toxic and a known carcinogen. Toll-like receptors (TLRs), highly expressed by myeloid dendritic cells (DC), are key innate immune-surveillance molecules. Toll-like receptors not only sense pathogen-associated molecular patterns but also contribute to infections and cancer. To assess AFB1–TLR interactions on human myeloid DC, pure CD11c+ DC were generated from monocytes isolated from healthy individuals and then exposed to relevant level of AFB1 for 2 hours. Both quantitative polymerase chain reaction and flow cytometric assays were used to quantify, respectively, expression of TLR2 and TLR4 at the messenger RNA (mRNA) and protein levels in these DC. Levels of interleukin (IL) 1β, IL-6, and IL-10 were also analyzed in AFB1- and mock-treated DC. Compared to nontreated CD11c+ DC, expression levels of both TLR2 and TLR4 mRNA and proteins were significantly upregulated in AFB1-treated cells. Further, although IL-10 levels in AFB1-treated DC were similar to those in the mock-treated DC, the AFB1-exposed DC secreted higher amounts of IL-1β and IL-6. Dendritic cells are sensitive to environmentally relevant level of AFB1, and TLR2 and TLR4 are involved in sensing AFB1. Considering the broad roles of TLR2, TLR4, and DC in immunity and infections, our novel findings open a new door to understanding the molecular mechanisms and functional consequences of AFB1 in inducing immunodysregulation, immunotoxicity, and thus (non)infectious diseases in humans.
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Affiliation(s)
- Azam Mohammadi
- Department of Pathobiology, Sections Immunology and Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Veterinary Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Jalil Mehrzad
- Department of Pathobiology, Sections Immunology and Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
- Veterinary Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mahmoud Mahmoudi
- Immunology Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Marion Schneider
- Sektion Experimentelle Anästhesiologie, Universitätsklinikum Ulm, Ulm, Germany
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