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Overnight Corticosterone and Gene Expression in Mouse Hippocampus: Time Course during Resting Period. Int J Mol Sci 2023; 24:ijms24032828. [PMID: 36769150 PMCID: PMC9917930 DOI: 10.3390/ijms24032828] [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: 12/22/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
The aim of the experiment was to test the effect of an elevated level of glucocorticoids on the mouse hippocampal transcriptome after 12 h of treatment with corticosterone that was administered during an active phase of the circadian cycle. Additionally, we also tested the circadian changes in gene expression and the decay time of transcriptomic response to corticosterone. Gene expression was analyzed using microarrays. Obtained results show that transcriptomic responses to glucocorticoids are heterogeneous in terms of the decay time with some genes displaying persistent changes in expression during 9 h of rest. We have also found a considerable overlap between genes regulated by corticosterone and genes implicated previously in stress response. The examples of such genes are Acer2, Agt, Apod, Aqp4, Etnppl, Fabp7, Fam107a, Fjx1, Fmo2, Galnt15, Gjc2, Heph, Hes5, Htra1, Jdp2, Kif5a, Lfng, Lrg1, Mgp, Mt1, Pglyrp1, Pla2g3, Plin4, Pllp, Ptgds, Ptn, Slc2a1, Slco1c1, Sult1a1, Thbd and Txnip. This indicates that the applied model is a useful tool for the investigation of mechanisms underlying the stress response.
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2
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Dai X, Shen L. Advances and Trends in Omics Technology Development. Front Med (Lausanne) 2022; 9:911861. [PMID: 35860739 PMCID: PMC9289742 DOI: 10.3389/fmed.2022.911861] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/09/2022] [Indexed: 12/11/2022] Open
Abstract
The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.
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3
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Rabaglino MB, O’Doherty A, Bojsen-Møller Secher J, Lonergan P, Hyttel P, Fair T, Kadarmideen HN. Application of multi-omics data integration and machine learning approaches to identify epigenetic and transcriptomic differences between in vitro and in vivo produced bovine embryos. PLoS One 2021; 16:e0252096. [PMID: 34029343 PMCID: PMC8143403 DOI: 10.1371/journal.pone.0252096] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/09/2021] [Indexed: 01/16/2023] Open
Abstract
Pregnancy rates for in vitro produced (IVP) embryos are usually lower than for embryos produced in vivo after ovarian superovulation (MOET). This is potentially due to alterations in their trophectoderm (TE), the outermost layer in physical contact with the maternal endometrium. The main objective was to apply a multi-omics data integration approach to identify both temporally differentially expressed and differentially methylated genes (DEG and DMG), between IVP and MOET embryos, that could impact TE function. To start, four and five published transcriptomic and epigenomic datasets, respectively, were processed for data integration. Second, DEG from day 7 to days 13 and 16 and DMG from day 7 to day 17 were determined in the TE from IVP vs. MOET embryos. Third, genes that were both DE and DM were subjected to hierarchical clustering and functional enrichment analysis. Finally, findings were validated through a machine learning approach with two additional datasets from day 15 embryos. There were 1535 DEG and 6360 DMG, with 490 overlapped genes, whose expression profiles at days 13 and 16 resulted in three main clusters. Cluster 1 (188) and Cluster 2 (191) genes were down-regulated at day 13 or day 16, respectively, while Cluster 3 genes (111) were up-regulated at both days, in IVP embryos compared to MOET embryos. The top enriched terms were the KEGG pathway "focal adhesion" in Cluster 1 (FDR = 0.003), and the cellular component: "extracellular exosome" in Cluster 2 (FDR<0.0001), also enriched in Cluster 1 (FDR = 0.04). According to the machine learning approach, genes in Cluster 1 showed a similar expression pattern between IVP and less developed (short) MOET conceptuses; and between MOET and DKK1-treated (advanced) IVP conceptuses. In conclusion, these results suggest that early conceptuses derived from IVP embryos exhibit epigenomic and transcriptomic changes that later affect its elongation and focal adhesion, impairing post-transfer survival.
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Affiliation(s)
- Maria B. Rabaglino
- Quantitative Genetics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
| | - Alan O’Doherty
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Jan Bojsen-Møller Secher
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Patrick Lonergan
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Poul Hyttel
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Trudee Fair
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Haja N. Kadarmideen
- Quantitative Genetics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Lyngby, Denmark
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4
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Saez-Lopez C, Villena JA, Simó R, Selva DM. Sex hormone-binding globulin overexpression protects against high-fat diet-induced obesity in transgenic male mice. J Nutr Biochem 2020; 85:108480. [PMID: 32795655 DOI: 10.1016/j.jnutbio.2020.108480] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 07/20/2020] [Accepted: 07/27/2020] [Indexed: 11/30/2022]
Abstract
Obese subjects of all ages and sex have reduced plasma SHBG levels. Whether these low plasma SHBG levels play a role in obesity development is unknown. In the present work we wanted to explore if SHBG overexpression could prevent obesity development induced by high fat diet (HFD). To do so, we fed humanized SHBG transgenic male mice and their wild-type littermates with control diet (CD) or HFD over the course of 8 weeks. The results showed that SHBG overexpression protected against body weight gain and fat accumulation induced by HFD. In addition, SHBG overexpression also abrogated the increase in insulin, leptin and resistin levels, as well as the reduction in adiponectin, induced by HFD. Mechanistically, the SHBG protection against HFD-induced obesity was achieved by stimulating lipolysis in white adipose tissue. Furthermore, we have demonstrated the SHBG cell-autonomous effect using human primary visceral adipocytes. Taking together, our results demonstrate that SHBG overexpression protects against diet-induced obesity and improves the metabolic profile of male mice fed a HFD diet.
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Affiliation(s)
- Cristina Saez-Lopez
- Diabetes and Metabolism Research Unit, Vall Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona and CIBERDEM (ISCIII), Barcelona, Spain
| | - Josep A Villena
- Laboratory of Metabolism and Obesity, Vall Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona and CIBERDEM (ISCIII), Barcelona, Spain
| | - Rafael Simó
- Diabetes and Metabolism Research Unit, Vall Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona and CIBERDEM (ISCIII), Barcelona, Spain
| | - David M Selva
- Diabetes and Metabolism Research Unit, Vall Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona and CIBERDEM (ISCIII), Barcelona, Spain.
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5
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Vincow ES, Thomas RE, Merrihew GE, Shulman NJ, Bammler TK, MacDonald JW, MacCoss MJ, Pallanck LJ. Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective. Autophagy 2019; 15:1592-1605. [PMID: 30865561 DOI: 10.1080/15548627.2019.1586258] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The destruction of mitochondria through macroautophagy (autophagy) has been recognised as a major route of mitochondrial protein degradation since its discovery more than 50 years ago, but fundamental questions remain unanswered. First, how much mitochondrial protein turnover occurs through auto-phagy? Mitochondrial proteins are also degraded by nonautophagic mechanisms, and the proportion of mitochondrial protein turnover that occurs through autophagy is still unknown. Second, does auto-phagy degrade mitochondrial proteins uniformly or selectively? Autophagy was originally thought to degrade all mitochondrial proteins at the same rate, but recent work suggests that mitochondrial autophagy may be protein selective. To investigate these questions, we used a proteomics-based approach in the fruit fly Drosophila melanogaster, comparing mitochondrial protein turnover rates in autophagy-deficient Atg7 mutants and controls. We found that ~35% of mitochondrial protein turnover occurred via autophagy. Similar analyses using parkin mutants revealed that parkin-dependent mitophagy accounted for ~25% of mitochondrial protein turnover, suggesting that most mitochondrial autophagy specifically eliminates dysfunctional mitochondria. We also found that our results were incompatible with uniform autophagic turnover of mitochondrial proteins and consistent with protein-selective autophagy. In particular, the autophagic turnover rates of individual mitochondrial proteins varied widely, and only a small amount of the variation could be attributed to tissue differences in mitochondrial composition and autophagy rate. Furthermore, analyses comparing autophagy-deficient and control human fibroblasts revealed diverse autophagy-dependent turnover rates even in homogeneous cells. In summary, our work indicates that autophagy acts selectively on mitochondrial proteins, and that most mitochondrial protein turnover occurs through non-autophagic processes. Abbreviations: Atg5: Autophagy-related 5 (Drosophila); ATG5: autophagy related 5 (human); Atg7: Autophagy-related 7 (Drosophila); ATG7: autophagy related 7 (human); DNA: deoxyribonucleic acid; ER: endoplasmic reticulum; GFP: green fluorescent protein; MS: mass spectrometry; park: parkin (Drosophila); Pink1: PTEN-induced putative kinase 1 (Drosophila); PINK1: PTEN-induced kinase 1 (human); PRKN: parkin RBR E3 ubiquitin protein ligase (human); RNA: ribonucleic acid; SD: standard deviation; Ub: ubiquitin/ubiquitinated; WT: wild-type; YME1L: YME1 like ATPase (Drosophila); YME1L1: YME1 like 1 ATPase (human).
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Affiliation(s)
- Evelyn S Vincow
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Ruth E Thomas
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Gennifer E Merrihew
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Nicholas J Shulman
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Theo K Bammler
- b Department of Environmental and Occupational Health Sciences, University of Washington , Seattle , WA , USA
| | - James W MacDonald
- b Department of Environmental and Occupational Health Sciences, University of Washington , Seattle , WA , USA
| | - Michael J MacCoss
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Leo J Pallanck
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
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6
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Choi JE, Verhaegen ME, Yazdani S, Malik R, Harms PW, Mangelberger D, Tien J, Cao X, Wang Y, Cieślik M, Gurkan J, Yazdani M, Jing X, Juckette K, Su F, Wang R, Zhou B, Apel IJ, Wang S, Dlugosz AA, Chinnaiyan AM. Characterizing the Therapeutic Potential of a Potent BET Degrader in Merkel Cell Carcinoma. Neoplasia 2019; 21:322-330. [PMID: 30797188 PMCID: PMC6384317 DOI: 10.1016/j.neo.2019.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 12/21/2022]
Abstract
Studies on the efficacy of small molecule inhibitors in Merkel cell carcinoma (MCC) have been limited and largely inconclusive. In this study, we investigated the therapeutic potential of a potent BET degrader, BETd-246, in the treatment of MCC. We found that MCC cell lines were significantly more sensitive to BETd-246 than to BET inhibitor treatment. Therapeutic targeting of BET proteins resulted in a loss of "MCC signature" genes but not MYC expression as previously described irrespective of Merkel cell polyomavirus (MCPyV) status. In MCPyV+ MCC cells, BETd-246 alone suppressed downstream targets in the MCPyV-LT Ag axis. We also found enrichment of HOX and cell cycle genes in MCPyV- MCC cell lines that were intrinsically resistant to BETd-246. Our findings uncover a requirement for BET proteins in maintaining MCC lineage identity and point to the potential utility of BET degraders for treating MCC.
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MESH Headings
- Acetanilides/pharmacology
- Antigens, Viral, Tumor/genetics
- Antigens, Viral, Tumor/metabolism
- Carcinoma, Merkel Cell/drug therapy
- Carcinoma, Merkel Cell/etiology
- Carcinoma, Merkel Cell/metabolism
- Carcinoma, Merkel Cell/pathology
- Cell Cycle/genetics
- Cell Line, Tumor
- Dose-Response Relationship, Drug
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Genes, Homeobox
- Heterocyclic Compounds, 3-Ring/pharmacology
- Humans
- Merkel cell polyomavirus/physiology
- Polyomavirus Infections/complications
- Polyomavirus Infections/virology
- Proteins/antagonists & inhibitors
- Proteins/metabolism
- Proteolysis
- Skin Neoplasms/drug therapy
- Skin Neoplasms/etiology
- Skin Neoplasms/metabolism
- Skin Neoplasms/pathology
- Transcriptome
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Affiliation(s)
- Jae Eun Choi
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Cancer Biology Program, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Sahr Yazdani
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Malik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Paul W Harms
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Dermatology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jean Tien
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yuping Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Marcin Cieślik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan Gurkan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Mishaal Yazdani
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaojun Jing
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Kristin Juckette
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Bing Zhou
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ingrid J Apel
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shaomeng Wang
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Andrzej A Dlugosz
- Department of Dermatology, University of Michigan, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA; Department of Urology, University of Michigan, Ann Arbor, MI, USA.
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7
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Stevens JR, Herrick JS, Wolff RK, Slattery ML. Power in pairs: assessing the statistical value of paired samples in tests for differential expression. BMC Genomics 2018; 19:953. [PMID: 30572829 PMCID: PMC6302489 DOI: 10.1186/s12864-018-5236-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/09/2018] [Indexed: 12/19/2022] Open
Abstract
Background When genomics researchers design a high-throughput study to test for differential expression, some biological systems and research questions provide opportunities to use paired samples from subjects, and researchers can plan for a certain proportion of subjects to have paired samples. We consider the effect of this paired samples proportion on the statistical power of the study, using characteristics of both count (RNA-Seq) and continuous (microarray) expression data from a colorectal cancer study. Results We demonstrate that a higher proportion of subjects with paired samples yields higher statistical power, for various total numbers of samples, and for various strengths of subject-level confounding factors. In the design scenarios considered, the statistical power in a fully-paired design is substantially (and in many cases several times) greater than in an unpaired design. Conclusions For the many biological systems and research questions where paired samples are feasible and relevant, substantial statistical power gains can be achieved at the study design stage when genomics researchers plan on using paired samples from the largest possible proportion of subjects. Any cost savings in a study design with unpaired samples are likely accompanied by underpowered and possibly biased results. Electronic supplementary material The online version of this article (10.1186/s12864-018-5236-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John R Stevens
- Department of Mathematics and Statistics, Utah State University, Logan, UT, USA.
| | - Jennifer S Herrick
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Roger K Wolff
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Martha L Slattery
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
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8
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Narrandes S, Xu W. Gene Expression Detection Assay for Cancer Clinical Use. J Cancer 2018; 9:2249-2265. [PMID: 30026820 PMCID: PMC6036716 DOI: 10.7150/jca.24744] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/15/2018] [Indexed: 12/23/2022] Open
Abstract
Cancer is a genetic disease where genetic variations cause abnormally functioning genes that appear to alter expression. Proteins, the final products of gene expression, determine the phenotypes and biological processes. Therefore, detecting gene expression levels can be used for cancer diagnosis, prognosis, and treatment prediction in a clinical setting. In this review, we investigated six gene expression assay systems (qRT-PCR, DNA microarray, nCounter, RNA-Seq, FISH, and tissue microarray) that are currently being used in clinical cancer studies. Some of these methods are also commonly used in a modified way; for example, detection of DNA content or protein expression. Herein, we discuss their principles, sample preparation, design, quantification and sensitivity, data analysis, time for sample preparation and processing, and cost. We also compared these methods according to their sample selection, particularly for the feasibility of using formalin-fixed paraffin-embedded (FFPE) samples, which are routinely archived for clinical cancer studies. We intend to provide a guideline for choosing an assay method with respect to its oncological applications in a clinical setting.
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Affiliation(s)
- Shavira Narrandes
- Departments of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada.,Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Canada
| | - Wayne Xu
- Departments of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada.,Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Canada.,College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
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9
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Begum G, Otsu M, Ahmed U, Ahmed Z, Stevens A, Fulton D. NF-Y-dependent regulation of glutamate receptor 4 expression and cell survival in cells of the oligodendrocyte lineage. Glia 2018; 66:1896-1914. [PMID: 29704264 PMCID: PMC6220837 DOI: 10.1002/glia.23446] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 03/14/2018] [Accepted: 04/11/2018] [Indexed: 12/15/2022]
Abstract
Glutamate receptor subunit 4 (GluA4) is highly expressed by neural cells sensitive to excitotoxicity, and is the predominant subunit expressed by oligodendrocyte precursor cells (OPC) during a key period of vulnerability to hypoxic‐ischemic injury. Therefore, transcriptional networks downstream of excitotoxic GluA4 activation represent a promising area for therapeutic intervention. In this work, we identify the CCAAT binding transcription factor NF‐Yb as a novel transcriptional regulator of Gria4 (GluA4 gene), and a controller of excitotoxic death in the oligodendroglial lineage. We describe a novel regulatory region within Gria4 containing CCAAT sequences whose binding by NF‐Yb is regulated by excitotoxicity. Excitotoxicity‐induced alterations in NF‐Yb binding are associated with changes in Gria4 transcription, while knockdown of NF‐Yb alters the transcription of reporter constructs containing this regulatory region. Data from immortalized and primary OPC reveal that RNAi and pharmacological disruption of NF‐Yb alter Gria4 transcription, with the latter inducing apoptosis and influencing a set of apoptotic genes similarly regulated during excitotoxicity. These data provide the first definition of a trans‐acting mechanism regulating Gria4, and identify the NF‐Y network as a potential source of pharmacological targets for promoting OPC survival.
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Affiliation(s)
- Ghazala Begum
- Neuroscience and Ophthalmology Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Masahiro Otsu
- Neuroscience and Ophthalmology Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Usman Ahmed
- Neuroscience and Ophthalmology Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Zubair Ahmed
- Neuroscience and Ophthalmology Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Adam Stevens
- Division of Developmental Biology & Medicine, Faculty of Biology, Medicine & Health, University of Manchester, Manchester Academic Health Sciences Centre, Manchester M13 9PL, United Kingdom
| | - Daniel Fulton
- Neuroscience and Ophthalmology Research Group, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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10
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Hypomethylating agents synergize with irinotecan to improve response to chemotherapy in colorectal cancer cells. PLoS One 2017; 12:e0176139. [PMID: 28445481 PMCID: PMC5405959 DOI: 10.1371/journal.pone.0176139] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/05/2017] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer death in the United States. In the metastatic setting, the majority of patients respond to initial therapies but eventually develop resistance and progress. In this study, we test the hypothesis that priming with epigenetic therapy sensitizes CRC cell lines, which were previously resistant to subsequent chemotherapeutic agents. When multiple CRC cell lines are first exposed to 500 nM of the DNA demethylating agent, 5-aza-cytidine (AZA) in-vitro, and the cells then established as in-vivo xenografts in untreated NOD-SCID mice; there is an enhanced response to cytotoxic chemotherapy with agents commonly used in CRC treatment. For irinotecan (IRI), growth diminished by 16–62 fold as assessed, by both proliferation (IC50) and anchorage independent cell growth soft agar assays. Treatment of resistant HCT116 cell line along with in-vivo, for CRC line xenografts, AZA plus IRI again exhibits this synergistic response with significant improvement in survival and tumor regression in the mice. Genome-wide expression correlates changes in pathways for cell adhesion and DNA repair with the above responses. A Phase 1/2 clinical trial testing this concept is already underway testing the clinical efficacy of this concept in IRI resistant, metastatic CRC (NCT01896856).
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11
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Haggard DE, Das SR, Tanguay RL. Comparative Toxicogenomic Responses to the Flame Retardant mITP in Developing Zebrafish. Chem Res Toxicol 2016; 30:508-515. [PMID: 27957850 DOI: 10.1021/acs.chemrestox.6b00423] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Monosubstituted isopropylated triaryl phosphate (mITP) is a major component of Firemaster 550, an additive flame retardant mixture commonly used in polyurethane foams. Developmental toxicity studies in zebrafish established mITP as the most toxic component of FM 550, which causes pericardial edema and heart looping failure. Mechanistic studies showed that mITP is an aryl hydrocarbon receptor (AhR) ligand; however, the cardiotoxic effects of mITP were independent of the AhR. We performed comparative whole genome transcriptomics in wild-type and ahr2hu3335 zebrafish, which lack functional ahr2, to identify transcriptional signatures causally involved in the mechanism of mITP-induced cardiotoxicity. Regardless of ahr2 status, mITP exposure resulted in decreased expression of transcripts related to the synthesis of all-trans-retinoic acid and a host of Hox genes. Clustered gene ontology enrichment analysis showed unique enrichment in biological processes related to xenobiotic metabolism and response to external stimuli in wild-type samples. Transcript enrichments overlapping both genotypes involved the retinoid metabolic process and sensory/visual perception biological processes. Examination of the gene-gene interaction network of the differentially expressed transcripts in both genetic backgrounds demonstrated a strong AhR interaction network specific to wild-type samples, with overlapping genes regulated by retinoic acid receptors (RARs). A transcriptome analysis of control ahr2-null zebrafish identified potential cross-talk among AhR, Nrf2, and Hif1α. Collectively, we confirmed that mITP is an AhR ligand and present evidence in support of our hypothesis that mITP's developmental cardiotoxic effects are mediated by inhibition at the RAR level.
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Affiliation(s)
- Derik E Haggard
- Department of Environmental and Molecular Toxicology, Oregon State University , Corvallis, Oregon 97333, United States
| | - Siba R Das
- Pacific Northwest Diabetes Research Institute , Seattle, Washington 98122, United States
| | - Robert L Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University , Corvallis, Oregon 97333, United States
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Transcriptomic Analysis of Persistent Infection with Foot-and-Mouth Disease Virus in Cattle Suggests Impairment of Apoptosis and Cell-Mediated Immunity in the Nasopharynx. PLoS One 2016; 11:e0162750. [PMID: 27643611 PMCID: PMC5028045 DOI: 10.1371/journal.pone.0162750] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/26/2016] [Indexed: 12/15/2022] Open
Abstract
In order to investigate the mechanisms of persistent foot-and-mouth disease virus (FMDV) infection in cattle, transcriptome alterations associated with the FMDV carrier state were characterized using a bovine whole-transcriptome microarray. Eighteen cattle (8 vaccinated with a recombinant FMDV A vaccine, 10 non-vaccinated) were challenged with FMDV A24 Cruzeiro, and the gene expression profiles of nasopharyngeal tissues collected between 21 and 35 days after challenge were compared between 11 persistently infected carriers and 7 non-carriers. Carriers and non-carriers were further compared to 2 naïve animals that had been neither vaccinated nor challenged. At a controlled false-discovery rate of 10% and a minimum difference in expression of 50%, 648 genes were differentially expressed between FMDV carriers and non-carriers, and most (467) had higher expression in carriers. Among these, genes associated with cellular proliferation and the immune response-such as chemokines, cytokines and genes regulating T and B cells-were significantly overrepresented. Differential gene expression was significantly correlated between non-vaccinated and vaccinated animals (biological correlation +0.97), indicating a similar transcriptome profile across these groups. Genes related to prostaglandin E2 production and the induction of regulatory T cells were overexpressed in carriers. In contrast, tissues from non-carrier animals expressed higher levels of complement regulators and pro-apoptotic genes that could promote virus clearance. Based on these findings, we propose a working hypothesis for FMDV persistence in nasopharyngeal tissues of cattle, in which the virus may be maintained by an impairment of apoptosis and the local suppression of cell-mediated antiviral immunity by inducible regulatory T cells.
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Koli K, Sutinen E, Rönty M, Rantakari P, Fortino V, Pulkkinen V, Greco D, Sipilä P, Myllärniemi M. Gremlin-1 Overexpression in Mouse Lung Reduces Silica-Induced Lymphocyte Recruitment - A Link to Idiopathic Pulmonary Fibrosis through Negative Correlation with CXCL10 Chemokine. PLoS One 2016; 11:e0159010. [PMID: 27428020 PMCID: PMC4948891 DOI: 10.1371/journal.pone.0159010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/25/2016] [Indexed: 12/24/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by activation and injury of epithelial cells, the accumulation of connective tissue and changes in the inflammatory microenvironment. The bone morphogenetic protein (BMP) inhibitor protein gremlin-1 is associated with the progression of fibrosis both in human and mouse lung. We generated a transgenic mouse model expressing gremlin-1 in type II lung epithelial cells using the surfactant protein C (SPC) promoter and the Cre-LoxP system. Gremlin-1 protein expression was detected specifically in the lung after birth and did not result in any signs of respiratory insufficiency. Exposure to silicon dioxide resulted in reduced amounts of lymphocyte aggregates in transgenic lungs while no alteration in the fibrotic response was observed. Microarray gene expression profiling and analyses of bronchoalveolar lavage fluid cytokines indicated a reduced lymphocytic response and a downregulation of interferon-induced gene program. Consistent with reduced Th1 response, there was a downregulation of the mRNA and protein expression of the anti-fibrotic chemokine CXCL10, which has been linked to IPF. In human IPF patient samples we also established a strong negative correlation in the mRNA expression levels of gremlin-1 and CXCL10. Our results suggest that in addition to regulation of epithelial-mesenchymal crosstalk during tissue injury, gremlin-1 modulates inflammatory cell recruitment and anti-fibrotic chemokine production in the lung.
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Affiliation(s)
- Katri Koli
- Research Programs Unit, Translational Cancer Biology, University of Helsinki, Helsinki, Finland
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Eva Sutinen
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Helsinki, Finland
- University of Helsinki and Helsinki University Hospital, Heart and Lung Center, Department of Pulmonary Medicine, Helsinki, Finland
| | - Mikko Rönty
- Department of Pathology, University of Helsinki and Fimlab laboratories, Pathology, Tampere, Finland
| | - Pia Rantakari
- MediCity Research Laboratory, University of Turku, Turku, Finland
| | - Vittorio Fortino
- Unit of Systems Toxicology and Nanosafety Centre, Finnish Institute of Occupational Health (FIOH), Helsinki, Finland
| | - Ville Pulkkinen
- University of Helsinki and Helsinki University Hospital, Heart and Lung Center, Department of Pulmonary Medicine, Helsinki, Finland
| | - Dario Greco
- Unit of Systems Toxicology and Nanosafety Centre, Finnish Institute of Occupational Health (FIOH), Helsinki, Finland
| | - Petra Sipilä
- Department of Physiology, Institute of Biomedicine and Turku Center for Disease Modeling, University of Turku, Turku, Finland
| | - Marjukka Myllärniemi
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Helsinki, Finland
- University of Helsinki and Helsinki University Hospital, Heart and Lung Center, Department of Pulmonary Medicine, Helsinki, Finland
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Fernández-Escobar M, Baldanta S, Reyburn H, Guerra S. Use of functional genomics to understand replication deficient poxvirus-host interactions. Virus Res 2016; 216:1-15. [PMID: 26519757 DOI: 10.1016/j.virusres.2015.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 10/22/2022]
Abstract
High-throughput genomics technologies are currently being used to study a wide variety of viral infections, providing insight into which cellular genes and pathways are regulated after infection, and how these changes are related, or not, to efficient elimination of the pathogen. This article will focus on how gene expression studies of infections with non-replicative poxviruses currently used as vaccine vectors provide a global perspective of the molecular events associated with the viral infection in human cells. These high-throughput genomics approaches have the potential to lead to the identification of specific new properties of the viral vector or novel cellular targets that may aid in the development of more effective pox-derived vaccines and antivirals.
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Affiliation(s)
- Mercedes Fernández-Escobar
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma, E-28029 Madrid, Spain
| | - Sara Baldanta
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma, E-28029 Madrid, Spain
| | - Hugh Reyburn
- Department of Immunology and Oncology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus Universidad Autónoma, E-28049 Madrid, Spain
| | - Susana Guerra
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma, E-28029 Madrid, Spain.
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Bell AM, Bukhari SA, Sanogo YO. Natural variation in brain gene expression profiles of aggressive and nonaggressive individual sticklebacks. BEHAVIOUR 2016; 153:1723-1743. [PMID: 29046592 DOI: 10.1163/1568539x-00003393] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within many species, some individuals are consistently more aggressive than others. We examine whether there are differences in brain gene expression between aggressive versus nonaggressive behavioural types of individuals within a natural population of male three-spined sticklebacks (Gasterosteus aculeatus). We compared gene expression profiles of aggressive male sticklebacks to nonaggressive males in four regions of the brain (brainstem, cerebellum, diencephalon and telencephalon). Relatively few genes were differentially expressed between behavioural types in telencephalon, cerebellum and diencephalon, but hundreds of genes were differentially expressed in brainstem, a brain area involved in detecting threats. Six genes that were differentially expressed in response to a territorial intrusion in a previous study were also differentially expressed between behavioural types in this study, implying primarily non-shared but some shared molecular mechanisms. Our findings offer new insights into the molecular causes and correlates of behavioural plasticity and individual variation in behaviour.
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Affiliation(s)
- Alison M Bell
- School of Integrative Biology, Program in Ecology, Evolution and Conservation, Program in Neuroscience, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, IL, USA
| | - Syed Abbas Bukhari
- Illinois Informatics Program, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana Champaign, IL, USA
| | - Yibayiri Osee Sanogo
- Genomics Core, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
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16
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Khalighi M, Dermauw W, Wybouw N, Bajda S, Osakabe M, Tirry L, Van Leeuwen T. Molecular analysis of cyenopyrafen resistance in the two-spotted spider mite Tetranychus urticae. PEST MANAGEMENT SCIENCE 2016; 72:103-112. [PMID: 26118668 DOI: 10.1002/ps.4071] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 06/11/2015] [Accepted: 06/23/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Cyenopyrafen is a recently developed acaricide with a new mode of action as a complex II inhibitor. However, it was recently shown that cross-resistance to cyenopyrafen can occur in resistant field strains of Tetranychus urticae, which might be linked to the previous use of classical METI acaricides. Here, we selected for cyenopyrafen resistance and studied the molecular mechanisms that underlie resistance. RESULTS Selection for cyenopyrafen resistance confers cross-resistance to the complex II inhibitor cyflumetofen, but also to pyridaben, a frequently used complex I inhibitor. Cyenopyrafen resistance is highly synergised by piperonyl butoxide, and a 15-fold higher P450 activity was detected in the resistant strain. Target-site resistance was not detected. Genome-wide gene expression data, followed by a meta-analysis of previously obtained gene expression data, revealed the overexpression specifically of CYP392A11 and CYP392A12. CONCLUSIONS Cyenopyrafen resistance is strongly linked to the overexpression of two P450s, which probably explains the observed cross-resistance. This information is highly valuable, as the novel complex II inhibitors cyenopyrafen and cyflumetofen are in the process of worldwide registration. The role of both CYP392A11 and CYP392A12 should be further supported by functional expression, but they are very promising candidates as molecular diagnostic markers for monitoring cyenopyrafen susceptibility in the field.
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Affiliation(s)
- Mousaalreza Khalighi
- Department of Crop Protection, Faculty of Bio-science Engineering, Ghent University, Ghent, Belgium
| | - Wannes Dermauw
- Department of Crop Protection, Faculty of Bio-science Engineering, Ghent University, Ghent, Belgium
| | - Nicky Wybouw
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Sabina Bajda
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Masahiro Osakabe
- Laboratory of Ecological Information, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Luc Tirry
- Department of Crop Protection, Faculty of Bio-science Engineering, Ghent University, Ghent, Belgium
| | - Thomas Van Leeuwen
- Department of Crop Protection, Faculty of Bio-science Engineering, Ghent University, Ghent, Belgium
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
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17
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The Effect of Acute and Chronic Social Stress on the Hippocampal Transcriptome in Mice. PLoS One 2015; 10:e0142195. [PMID: 26556046 PMCID: PMC4640871 DOI: 10.1371/journal.pone.0142195] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 10/19/2015] [Indexed: 12/19/2022] Open
Abstract
Psychogenic stress contributes to the formation of brain pathology. Using gene expression microarrays, we analyzed the hippocampal transcriptome of mice subjected to acute and chronic social stress of different duration. The longest period of social stress altered the expression of the highest number of genes and most of the stress-induced changes in transcription were reversible after 5 days of rest. Chronic stress affected genes involved in the functioning of the vascular system (Alas2, Hbb-b1, Hba-a2, Hba-a1), injury response (Vwf, Mgp, Cfh, Fbln5, Col3a1, Ctgf) and inflammation (S100a8, S100a9, Ctla2a, Ctla2b, Lcn2, Lrg1, Rsad2, Isg20). The results suggest that stress may affect brain functions through the stress-induced dysfunction of the vascular system. An important issue raised in our work is also the risk of the contamination of brain tissue samples with choroid plexus. Such contamination would result in a consistent up- or down-regulation of genes, such as Ttr, Igf2, Igfbp2, Prlr, Enpp2, Sostdc1, 1500015O10RIK (Ecrg4), Kl, Clic6, Kcne2, F5, Slc4a5, and Aqp1. Our study suggests that some of the previously reported, supposedly specific changes in hippocampal gene expression, may be a result of the inclusion of choroid plexus in the hippocampal samples.
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Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 2015; 43:e47. [PMID: 25605792 PMCID: PMC4402510 DOI: 10.1093/nar/gkv007] [Citation(s) in RCA: 22035] [Impact Index Per Article: 2448.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Accepted: 01/06/2015] [Indexed: 02/06/2023] Open
Abstract
limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
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Affiliation(s)
- Matthew E Ritchie
- Molecular Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia Department of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Belinda Phipson
- Murdoch Childrens Research Institute, Royal Children's Hospital, 50 Flemington Road, Parkville, Victoria 3052, Australia
| | - Di Wu
- Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, MA 02138-2901, USA
| | - Yifang Hu
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Charity W Law
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Wei Shi
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia Department of Computing and Information Systems, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gordon K Smyth
- Department of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria 3010, Australia Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
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Rydman EM, Ilves M, Koivisto AJ, Kinaret PAS, Fortino V, Savinko TS, Lehto MT, Pulkkinen V, Vippola M, Hämeri KJ, Matikainen S, Wolff H, Savolainen KM, Greco D, Alenius H. Inhalation of rod-like carbon nanotubes causes unconventional allergic airway inflammation. Part Fibre Toxicol 2014; 11:48. [PMID: 25318534 PMCID: PMC4215016 DOI: 10.1186/s12989-014-0048-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 08/27/2014] [Indexed: 12/28/2022] Open
Abstract
Background Carbon nanotubes (CNT) represent a great promise for technological and industrial development but serious concerns on their health effects have also emerged. Rod-shaped CNT are, in fact, able to induce asbestos-like pathogenicity in mice including granuloma formation in abdominal cavity and sub-pleural fibrosis. Exposure to CNT, especially in the occupational context, happens mainly by inhalation. However, little is known about the possible effects of CNT on pulmonary allergic diseases, such as asthma. Methods We exposed mice by inhalation to two types of multi-walled CNT, rigid rod-like and flexible tangled CNT, for four hours a day once or on four consecutive days. Early events were monitored immediately and 24 hours after the single inhalation exposure and the four day exposure mimicked an occupational work week. Mast cell deficient mice were used to evaluate the role of mast cells in the occurring inflammation. Results Here we show that even a short-term inhalation of the rod-like CNT induces novel innate immunity-mediated allergic-like airway inflammation in healthy mice. Marked eosinophilia was accompanied by mucus hypersecretion, AHR and the expression of Th2-type cytokines. Exploration of the early events by transcriptomics analysis reveals that a single 4-h exposure to rod-shaped CNT, but not to tangled CNT, causes a radical up-regulation of genes involved in innate immunity and cytokine/chemokine pathways. Mast cells were found to partially regulate the inflammation caused by rod-like CNT, but also alveaolar macrophages play an important role in the early stages. Conclusions These observations emphasize the diverse abilities of CNT to impact the immune system, and they should be taken into account for hazard assessment. Electronic supplementary material The online version of this article (doi:10.1186/s12989-014-0048-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elina M Rydman
- Nanosafety Research Centre, Finnish Institute of Occupational Health, Helsinki, Finland.
| | - Marit Ilves
- Nanosafety Research Centre, Finnish Institute of Occupational Health, Helsinki, Finland.
| | - Antti J Koivisto
- Nanosafety Research Centre, Finnish Institute of Occupational Health, Helsinki, Finland.
| | - Pia A S Kinaret
- Nanosafety Research Centre, Finnish Institute of Occupational Health, Helsinki, Finland.
| | - Vittorio Fortino
- Nanosafety Research Centre, Finnish Institute of Occupational Health, Helsinki, Finland.
| | - Terhi S Savinko
- Nanosafety Research Centre, Finnish Institute of Occupational Health, Helsinki, Finland.
| | - Maili T Lehto
- Nanosafety Research Centre, Finnish Institute of Occupational Health, Helsinki, Finland.
| | - Ville Pulkkinen
- Pulmonary Division, Department of Medicine, University of Helsinki, Helsinki, Finland.
| | - Minnamari Vippola
- Nanosafety Research Centre, Finnish Institute of Occupational Health, Helsinki, Finland. .,Department of Materials Science, Tampere University of Technology, Tampere, Finland.
| | - Kaarle J Hämeri
- Department of Physics, University of Helsinki, Helsinki, Finland.
| | - Sampsa Matikainen
- Nanosafety Research Centre, Finnish Institute of Occupational Health, Helsinki, Finland.
| | - Henrik Wolff
- Nanosafety Research Centre, Finnish Institute of Occupational Health, Helsinki, Finland.
| | - Kai M Savolainen
- Nanosafety Research Centre, Finnish Institute of Occupational Health, Helsinki, Finland.
| | - Dario Greco
- Nanosafety Research Centre, Finnish Institute of Occupational Health, Helsinki, Finland.
| | - Harri Alenius
- Nanosafety Research Centre, Finnish Institute of Occupational Health, Helsinki, Finland.
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Ahn SJ, Dermauw W, Wybouw N, Heckel DG, Van Leeuwen T. Bacterial origin of a diverse family of UDP-glycosyltransferase genes in the Tetranychus urticae genome. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 50:43-57. [PMID: 24727020 DOI: 10.1016/j.ibmb.2014.04.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/28/2014] [Accepted: 04/01/2014] [Indexed: 06/03/2023]
Abstract
UDP-glycosyltransferases (UGTs) catalyze the conjugation of a variety of small lipophilic molecules with uridine diphosphate (UDP) sugars, altering them into more water-soluble metabolites. Thereby, UGTs play an important role in the detoxification of xenobiotics and in the regulation of endobiotics. Recently, the genome sequence was reported for the two-spotted spider mite, Tetranychus urticae, a polyphagous herbivore damaging a number of agricultural crops. Although various gene families implicated in xenobiotic metabolism have been documented in T. urticae, UGTs so far have not. We identified 80 UGT genes in the T. urticae genome, the largest number of UGT genes in a metazoan species reported so far. Phylogenetic analysis revealed that lineage-specific gene expansions increased the diversity of the T. urticae UGT repertoire. Genomic distribution, intron-exon structure and structural motifs in the T. urticae UGTs were also described. In addition, expression profiling after host-plant shifts and in acaricide resistant lines supported an important role for UGT genes in xenobiotic metabolism. Expanded searches of UGTs in other arachnid species (Subphylum Chelicerata), including a spider, a scorpion, two ticks and two predatory mites, unexpectedly revealed the complete absence of UGT genes. However, a centipede (Subphylum Myriapoda) and a water flea and a crayfish (Subphylum Crustacea) contain UGT genes in their genomes similar to insect UGTs, suggesting that the UGT gene family might have been lost early in the Chelicerata lineage and subsequently re-gained in the tetranychid mites. Sequence similarity of T. urticae UGTs and bacterial UGTs and their phylogenetic reconstruction suggest that spider mites acquired UGT genes from bacteria by horizontal gene transfer. Our findings show a unique evolutionary history of the T. urticae UGT gene family among other arthropods and provide important clues to its functions in relation to detoxification and thereby host adaptation.
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Affiliation(s)
- Seung-Joon Ahn
- Department of Entomology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; National Institute of Horticultural and Herbal Science, Rural Development Administration, 441-440 Suwon, Korea.
| | - Wannes Dermauw
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - Nicky Wybouw
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Thomas Van Leeuwen
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, B-9000 Ghent, Belgium; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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Differential induction of apoptosis, interferon signaling, and phagocytosis in macrophages infected with a panel of attenuated and nonattenuated poxviruses. J Virol 2014; 88:5511-23. [PMID: 24599993 DOI: 10.1128/jvi.00468-14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Due to the essential role macrophages play in antiviral immunity, it is important to understand the intracellular and molecular processes that occur in macrophages following infection with various strains of vaccinia virus, particularly those used as vaccine vectors. Similarities as well as differences were found in macrophages infected with different poxvirus strains, particularly at the level of virus-induced apoptosis and the expression of immunomodulatory genes, as determined by microarray analyses. Interestingly, the attenuated modified vaccinia Ankara virus (MVA) was particularly efficient in triggering apoptosis and beta interferon (IFN-β) secretion and in inducing changes in the expression of genes associated with increased activation of innate immunity, setting it apart from the other five vaccinia virus strains tested. Taken together, these results increase our understanding of how these viruses interact with human macrophages, at the cellular and molecular levels, and suggest mechanisms that may underlie their utility as recombinant vaccine vectors. IMPORTANCE Our studies clearly demonstrate that there are substantial biological differences in the patterns of cellular gene expression between macrophages infected with different poxvirus strains and that these changes are due specifically to infection with the distinct viruses. For example, a clear induction in IFN-β mRNA was observed after infection with MVA but not with other poxviruses. Importantly, antiviral bioassays confirmed that MVA-infected macrophages secreted a high level of biologically active type I IFN. Similarly, the phagocytic capacity of macrophages was also specifically increased after infection with MVA. Although the main scope of this study was not to test the vaccine potential of MVA as there are several groups in the field working extensively on this aspect, the characteristics/phenotypes we observed at the in vitro level clearly highlight the inherent advantages that MVA possesses in comparison to other poxvirus strains.
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