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Tsuchiya M, Giuliani A, Brazhnik P. From Cell States to Cell Fates: Control of Cell State Transitions. Methods Mol Biol 2024; 2745:137-162. [PMID: 38060184 DOI: 10.1007/978-1-0716-3577-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
We examine the coordinated behavior of thousands of genes in cell fate transitions through genome expression as an integrated dynamical system using the concepts of self-organized criticality and coherent stochastic behavior. To quantify the effects of the collective behavior of genes, we adopted the flux balance approach and developed it in a new tool termed expression flux analysis (EFA). Here we describe this tool and demonstrate how its application to specific experimental genome-wide expression data provides new insights into the dynamics of the cell-fate transitions. Particularly, we show that in cell fate change, specific stochastic perturbations can spread over the entire system to guide distinct cell fate transitions through switching cyclic flux flow in the genome engine. Utilization of EFA enables us to elucidate a unified genomic mechanism for when and how cell-fate change occurs through critical transitions.
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Affiliation(s)
- Masa Tsuchiya
- SEIKO Life Science Laboratory, SEIKO Research Institute for Education, Osaka, Japan
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanitá, Rome, Italy
| | - Paul Brazhnik
- Academy of Integrated Science, Virginia Tech, Blacksburg, VA, USA
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2
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Cerri F, Gentile F, Clarelli F, Santoro S, Falzone YM, Dina G, Romano A, Domi T, Pozzi L, Fazio R, Podini P, Sorosina M, Carrera P, Esposito F, Riva N, Briani C, Cavallaro T, Filippi M, Quattrini A. Clinical and pathological findings in neurolymphomatosis: Preliminary association with gene expression profiles in sural nerves. Front Oncol 2022; 12:974751. [PMID: 36226068 PMCID: PMC9549065 DOI: 10.3389/fonc.2022.974751] [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: 06/21/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Although inflammation appears to play a role in neurolymphomatosis (NL), the mechanisms leading to degeneration in the peripheral nervous system are poorly understood. The purpose of this exploratory study was to identify molecular pathways underlying NL pathogenesis, combining clinical and neuropathological investigation with gene expression (GE) studies. We characterized the clinical and pathological features of eight patients with NL. We further analysed GE changes in sural nerve biopsies obtained from a subgroup of NL patients (n=3) and thirteen patients with inflammatory neuropathies as neuropathic controls. Based on the neuropathic symptoms and signs, NL patients were classified into three forms of neuropathy: chronic symmetrical sensorimotor polyneuropathy (SMPN, n=3), multiple mononeuropathy (MN, n=4) and acute motor-sensory axonal neuropathy (AMSAN, n=1). Predominantly diffuse malignant cells infiltration of epineurium was present in chronic SMPN, whereas endoneurial perivascular cells invasion was observed in MN. In contrast, diffuse endoneurium malignant cells localization occurred in AMSAN. We identified alterations in the expression of 1266 genes, with 115 up-regulated and 1151 down-regulated genes, which were mainly associated with ribosomal proteins (RP) and olfactory receptors (OR) signaling pathways, respectively. Among the top up-regulated genes were actin alpha 1 skeletal muscle (ACTA1) and desmin (DES). Similarly, in NL nerves ACTA1, DES and several RPs were highly expressed, associated with endothelial cells and pericytes abnormalities. Peripheral nerve involvement may be due to conversion towards a more aggressive phenotype, potentially explaining the poor prognosis. The candidate genes reported in this study may be a source of clinical biomarkers for NL.
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Affiliation(s)
- Federica Cerri
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Gentile
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Ferdinando Clarelli
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Santoro
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Yuri Matteo Falzone
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Giorgia Dina
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Romano
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Teuta Domi
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Laura Pozzi
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Raffaella Fazio
- Department of Neurology, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Paola Podini
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Melissa Sorosina
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Paola Carrera
- Division of Genetics and Cell Biology and Laboratory of Clinical Molecular Biology and Cytogenetics, Unit of Genomics for Human Disease Diagnosis, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Federica Esposito
- Department of Neurology, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Nilo Riva
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- Department of Neurology, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- *Correspondence: Nilo Riva, ; Angelo Quattrini,
| | - Chiara Briani
- Department of Neuroscience , University of Padova, Padova, Italy
| | - Tiziana Cavallaro
- Department of Neurology, Azienda Ospedaliera Universitaria Integrata, University Hospital G.B. Rossi, Verona, Italy
| | - Massimo Filippi
- Department of Neurology, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Angelo Quattrini
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- *Correspondence: Nilo Riva, ; Angelo Quattrini,
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Newaz K, Milenkovic T. Inference of a Dynamic Aging-related Biological Subnetwork via Network Propagation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:974-988. [PMID: 32897864 DOI: 10.1109/tcbb.2020.3022767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Gene expression (GE)data capture valuable condition-specific information ("condition" can mean a biological process, disease stage, age, patient, etc.)However, GE analyses ignore physical interactions between gene products, i.e., proteins. Because proteins function by interacting with each other, and because biological networks (BNs)capture these interactions, BN analyses are promising. However, current BN data fail to capture condition-specific information. Recently, GE and BN data have been integrated using network propagation (NP)to infer condition-specific BNs. However, existing NP-based studies result in a static condition-specific subnetwork, even though cellular processes are dynamic. A dynamic process of our interest is human aging. We use prominent existing NP methods in a new task of inferring a dynamic rather than static condition-specific (aging-related)subnetwork. Then, we study evolution of network structure with age - we identify proteins whose network positions significantly change with age and predict them as new aging-related candidates. We validate the predictions via e.g., functional enrichment analyses and literature search. Dynamic network inference via NP yields higher prediction quality than the only existing method for inferring a dynamic aging-related BN, which does not use NP. Our data and code are available at https://nd.edu/~cone/dynetinf.
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Tsuchiya M, Giuliani A, Zimatore G, Erenpreisa J, Yoshikawa K. A Unified Genomic Mechanism of Cell-Fate Change. Results Probl Cell Differ 2022; 70:35-69. [PMID: 36348104 DOI: 10.1007/978-3-031-06573-6_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The purpose of our studies is to elucidate the nature of massive control of the whole genome expression with a particular emphasis on cell-fate change. The whole genome expression is coordinated by the emergence of a critical point (CP: a peculiar set of biphasic genes) with the genome acting as an integrated dynamical system. In response to stimuli, the genome expression self-organizes into local sub-, near-, and super-critical states, each exhibiting distinct collective behaviors with its center of mass acting as a local attractor, coexisting with the whole genome attractor (GA). The CP serves as the organizing center of cell-fate change, and its activation makes local perturbation to spread over the genome affecting GA. The activation of CP is in turn elicited by genes with elevated temporal variance (oscillating-mode genes), normally in charge to keep genome expression at pace with microenvironment fluctuations. When oscillation exceeds a given threshold, the CP synchronizes with the GA driving genome expression state transition. The expression synchronization wave invading the entire genome is fostered by the fusion-splitting dynamics of silencing pericentromere-associated heterochromatin domains and the consequent folding-unfolding transitions of transcribing euchromatin domains. The proposed mechanism is a unified step toward a time-evolutional transition theory of biological regulation.
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Affiliation(s)
- Masa Tsuchiya
- SEIKO Life Science Laboratory, SEIKO Research Institute for Education, Osaka, Japan.
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanitá, Rome, Italy.
| | | | | | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
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Parikh HM, Elgzyri T, Alibegovic A, Hiscock N, Ekström O, Eriksson KF, Vaag A, Groop LC, Ström K, Hansson O. Relationship between insulin sensitivity and gene expression in human skeletal muscle. BMC Endocr Disord 2021; 21:32. [PMID: 33639916 PMCID: PMC7912896 DOI: 10.1186/s12902-021-00687-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Insulin resistance (IR) in skeletal muscle is a key feature of the pre-diabetic state, hypertension, dyslipidemia, cardiovascular diseases and also predicts type 2 diabetes. However, the underlying molecular mechanisms are still poorly understood. METHODS To explore these mechanisms, we related global skeletal muscle gene expression profiling of 38 non-diabetic men to a surrogate measure of insulin sensitivity, i.e. homeostatic model assessment of insulin resistance (HOMA-IR). RESULTS We identified 70 genes positively and 110 genes inversely correlated with insulin sensitivity in human skeletal muscle, identifying autophagy-related genes as positively correlated with insulin sensitivity. Replication in an independent study of 9 non-diabetic men resulted in 10 overlapping genes that strongly correlated with insulin sensitivity, including SIRT2, involved in lipid metabolism, and FBXW5 that regulates mammalian target-of-rapamycin (mTOR) and autophagy. The expressions of SIRT2 and FBXW5 were also positively correlated with the expression of key genes promoting the phenotype of an insulin sensitive myocyte e.g. PPARGC1A. CONCLUSIONS The muscle expression of 180 genes were correlated with insulin sensitivity. These data suggest that activation of genes involved in lipid metabolism, e.g. SIRT2, and genes regulating autophagy and mTOR signaling, e.g. FBXW5, are associated with increased insulin sensitivity in human skeletal muscle, reflecting a highly flexible nutrient sensing.
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Affiliation(s)
- Hemang M Parikh
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, 3650 Spectrum Blvd, Tampa, FL, 33612, USA.
- Department of Clinical Sciences, Diabetes & Endocrinology, Lund University, University Hospital Malmö, SE-20502, Malmö, Sweden.
| | - Targ Elgzyri
- Department of Clinical Sciences, Diabetes & Endocrinology, Lund University, University Hospital Malmö, SE-20502, Malmö, Sweden
| | | | - Natalie Hiscock
- Unilever Discover R & D, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Ola Ekström
- Department of Clinical Sciences, Diabetes & Endocrinology, Lund University, University Hospital Malmö, SE-20502, Malmö, Sweden
| | - Karl-Fredrik Eriksson
- Department of Clinical Sciences, Diabetes & Endocrinology, Lund University, University Hospital Malmö, SE-20502, Malmö, Sweden
| | - Allan Vaag
- Steno Diabetes Center, DK-2820, Gentofte, Denmark
| | - Leif C Groop
- Department of Clinical Sciences, Diabetes & Endocrinology, Lund University, University Hospital Malmö, SE-20502, Malmö, Sweden
- Finnish Institute of Molecular Medicine, FI-00014, University of Helsinki, Helsinki, Finland
| | - Kristoffer Ström
- Department of Clinical Sciences, Diabetes & Endocrinology, Lund University, University Hospital Malmö, SE-20502, Malmö, Sweden
- Swedish Winter Sports Research Centre, Mid Sweden University, SE-83125, Östersund, Sweden
| | - Ola Hansson
- Department of Clinical Sciences, Diabetes & Endocrinology, Lund University, University Hospital Malmö, SE-20502, Malmö, Sweden
- Finnish Institute of Molecular Medicine, FI-00014, University of Helsinki, Helsinki, Finland
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6
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Eagle GL, Herbert JMJ, Zhuang J, Oates M, Khan UT, Kitteringham NR, Clarke K, Park BK, Pettitt AR, Jenkins RE, Falciani F. Assessing technical and biological variation in SWATH-MS-based proteomic analysis of chronic lymphocytic leukaemia cells. Sci Rep 2021; 11:2932. [PMID: 33536534 PMCID: PMC7858606 DOI: 10.1038/s41598-021-82609-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/11/2021] [Indexed: 12/18/2022] Open
Abstract
Chronic lymphocytic leukaemia (CLL) exhibits variable clinical course and response to therapy, but the molecular basis of this variability remains incompletely understood. Data independent acquisition (DIA)-MS technologies, such as SWATH (Sequential Windowed Acquisition of all THeoretical fragments), provide an opportunity to study the pathophysiology of CLL at the proteome level. Here, a CLL-specific spectral library (7736 proteins) is described alongside an analysis of sample replication and data handling requirements for quantitative SWATH-MS analysis of clinical samples. The analysis was performed on 6 CLL samples, incorporating biological (IGHV mutational status), sample preparation and MS technical replicates. Quantitative information was obtained for 5169 proteins across 54 SWATH-MS acquisitions: the sources of variation and different computational approaches for batch correction were assessed. Functional enrichment analysis of proteins associated with IGHV mutational status showed significant overlap with previous studies based on gene expression profiling. Finally, an approach to perform statistical power analysis in proteomics studies was implemented. This study provides a valuable resource for researchers working on the proteomics of CLL. It also establishes a sound framework for the design of sufficiently powered clinical proteomics studies. Indeed, this study shows that it is possible to derive biologically plausible hypotheses from a relatively small dataset.
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Affiliation(s)
- Gina L Eagle
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - John M J Herbert
- Computational Biology Facility, University of Liverpool, Liverpool, UK
| | - Jianguo Zhuang
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Melanie Oates
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Umair T Khan
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,Department of Haemato-Oncology, Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, UK
| | - Neil R Kitteringham
- Department Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | - Kim Clarke
- Computational Biology Facility, University of Liverpool, Liverpool, UK
| | - B Kevin Park
- Department Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK
| | - Andrew R Pettitt
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,Department of Haemato-Oncology, Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, UK
| | - Rosalind E Jenkins
- Department Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, MRC Centre for Drug Safety Science, University of Liverpool, Liverpool, UK.
| | - Francesco Falciani
- Computational Biology Facility, University of Liverpool, Liverpool, UK. .,Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
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7
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Zhang Y, Archer KJ. Bayesian penalized cumulative logit model for high-dimensional data with an ordinal response. Stat Med 2020; 40:1453-1481. [PMID: 33336826 DOI: 10.1002/sim.8851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 01/15/2023]
Abstract
Many previous studies have identified associations between gene expression, measured using high-throughput genomic platforms, and quantitative or dichotomous traits. However, we note that health outcome and disease status measurements frequently appear on an ordinal scale, that is, the outcome is categorical but has inherent ordering. Identification of important genes may be useful for developing novel diagnostic and prognostic tools to predict or classify stage of disease. Gene expression data are usually high-dimensional, meaning that the number of genes is much larger than the sample size or number of patients. Herein we describe some existing frequentist methods for modeling an ordinal response in a high-dimensional predictor space. Following Tibshirani (1996), who described the LASSO estimate as the Bayesian posterior mode when the regression coefficients have independent Laplace priors, we propose a new approach for high-dimensional data with an ordinal response that is rooted in the Bayesian paradigm. We show that our proposed Bayesian approach outperforms existing frequentist methods through simulation studies. We then compare the performance of frequentist and Bayesian approaches using a study evaluating progression to hepatocellular carcinoma in hepatitis C infected patients.
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Affiliation(s)
- Yiran Zhang
- College of Public Health, The Ohio State University, Columbus, Ohio, USA
| | - Kellie J Archer
- College of Public Health, The Ohio State University, Columbus, Ohio, USA
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8
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Ni P, Clinkenbeard EL, Noonan ML, Richardville JM, McClintick J, Hato T, Janosevic D, Cheng YH, El-Achkar TM, Eadon MT, Dagher PC, White KE. Targeting fibroblast growth factor 23-responsive pathways uncovers controlling genes in kidney mineral metabolism. Kidney Int 2020; 99:598-608. [PMID: 33159963 DOI: 10.1016/j.kint.2020.10.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 09/21/2020] [Accepted: 10/09/2020] [Indexed: 12/17/2022]
Abstract
Fibroblast Growth Factor 23 (FGF23) is a bone-derived hormone that reduces kidney phosphate reabsorption and 1,25(OH)2 vitamin D synthesis via its required co-receptor alpha-Klotho. To identify novel genes that could serve as targets to control FGF23-mediated mineral metabolism, gene array and single-cell RNA sequencing were performed in wild type mouse kidneys. Gene array demonstrated that heparin-binding EGF-like growth factor (HBEGF) was significantly up-regulated following one-hour FGF23 treatment of wild type mice. Mice injected with HBEGF had phenotypes consistent with partial FGF23-mimetic activity including robust induction of Egr1, and increased Cyp24a1 mRNAs. Single cell RNA sequencing showed overlapping HBEGF and EGF-receptor expression mostly in the proximal tubule, and alpha-Klotho expression in proximal and distal tubule segments. In alpha-Klotho-null mice devoid of canonical FGF23 signaling, HBEGF injections significantly increased Egr1 and Cyp24a1 with correction of basally elevated Cyp27b1. Additionally, mice placed on a phosphate deficient diet to suppress FGF23 had endogenously increased Cyp27b1 mRNA, which was rescued in mice receiving HBEGF. In HEK293 cells with stable alpha-Klotho expression, FGF23 and HBEGF increased CYP24A1 mRNA expression. HBEGF, but not FGF23 bioactivity was blocked with EGF-receptor inhibition. Thus, our findings support that the paracrine/autocrine factor HBEGF could play novel roles in controlling genes downstream of FGF23 via targeting common signaling pathways.
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Affiliation(s)
- Pu Ni
- Department of Medical and Molecular Genetics, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Erica L Clinkenbeard
- Department of Medical and Molecular Genetics, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Megan L Noonan
- Department of Medical and Molecular Genetics, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Joseph M Richardville
- Department of Medical and Molecular Genetics, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jeanette McClintick
- Department of Biochemistry and Molecular Biology, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Takashi Hato
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Danielle Janosevic
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ying-Hua Cheng
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Tarek M El-Achkar
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Michael T Eadon
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Pierre C Dagher
- Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Kenneth E White
- Department of Medical and Molecular Genetics, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Department of Medicine, Division of Nephrology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
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9
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LaFavers KA, Macedo E, Garimella PS, Lima C, Khan S, Myslinski J, McClintick J, Witzmann FA, Winfree S, Phillips CL, Hato T, Dagher PC, Wu XR, El-Achkar TM, Micanovic R. Circulating uromodulin inhibits systemic oxidative stress by inactivating the TRPM2 channel. Sci Transl Med 2020; 11:11/512/eaaw3639. [PMID: 31578243 DOI: 10.1126/scitranslmed.aaw3639] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/26/2019] [Accepted: 08/22/2019] [Indexed: 12/21/2022]
Abstract
High serum concentrations of kidney-derived protein uromodulin [Tamm-Horsfall protein (THP)] have recently been shown to be independently associated with low mortality in both older adults and cardiac patients, but the underlying mechanism remains unclear. Here, we show that THP inhibits the generation of reactive oxygen species (ROS) both in the kidney and systemically. Consistent with this experimental data, the concentration of circulating THP in patients with surgery-induced acute kidney injury (AKI) correlated with systemic oxidative damage. THP in the serum dropped after AKI and was associated with an increase in systemic ROS. The increase in oxidant injury correlated with postsurgical mortality and need for dialysis. Mechanistically, THP inhibited the activation of the transient receptor potential cation channel, subfamily M, member 2 (TRPM2) channel. Furthermore, inhibition of TRPM2 in vivo in a mouse model mitigated the systemic increase in ROS during AKI and THP deficiency. Our results suggest that THP is a key regulator of systemic oxidative stress by suppressing TRPM2 activity, and our findings might help explain how circulating THP deficiency is linked with poor outcomes and increased mortality.
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Affiliation(s)
- Kaice A LaFavers
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Etienne Macedo
- Division of Nephrology-Hypertension, Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Pranav S Garimella
- Division of Nephrology-Hypertension, Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
| | - Camila Lima
- Division of Nephrology, Department of Medicine, University of Sao Paulo, Sao Paulo 05403, Brazil
| | - Shehnaz Khan
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jered Myslinski
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jeanette McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Frank A Witzmann
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Seth Winfree
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Carrie L Phillips
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Takashi Hato
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Pierre C Dagher
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Richard L. Roudebush VA Medical Center, Indianapolis, IN 46202, USA
| | - Xue-Ru Wu
- Departments of Urology and Pathology, New York University School of Medicine and Veterans Affairs, New York Harbor Healthcare System, Manhattan Campus, New York, NY 10010, USA
| | - Tarek M El-Achkar
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA. .,Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Richard L. Roudebush VA Medical Center, Indianapolis, IN 46202, USA.,Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Radmila Micanovic
- Division of Nephrology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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10
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Li G, Lin R, Egekwu C, Blakeslee J, Lin J, Pettengill E, Murphy AS, Peer WA, Islam N, Babst BA, Gao F, Komarov S, Tai YC, Coleman GD. Seasonal nitrogen remobilization and the role of auxin transport in poplar trees. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4512-4530. [PMID: 32161967 PMCID: PMC7382381 DOI: 10.1093/jxb/eraa130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 03/06/2020] [Indexed: 05/31/2023]
Abstract
Seasonal nitrogen (N) cycling in Populus, involves bark storage proteins (BSPs) that accumulate in bark phloem parenchyma in the autumn and decline when shoot growth resumes in the spring. Little is known about the contribution of BSPs to growth or the signals regulating N remobilization from BSPs. Knockdown of BSP accumulation via RNAi and N sink manipulations were used to understand how BSP storage influences shoot growth. Reduced accumulation of BSPs delayed bud break and reduced shoot growth following dormancy. Further, 13N tracer studies also showed that BSP accumulation is an important factor in N partitioning from senescing leaves to bark. Thus, BSP accumulation has a role in N remobilization during N partitioning both from senescing leaves to bark and from bark to expanding shoots once growth commences following dormancy. The bark transcriptome during BSP catabolism and N remobilization was enriched in genes associated with auxin transport and signaling, and manipulation of the source of auxin or auxin transport revealed a role for auxin in regulating BSP catabolism and N remobilization. Therefore, N remobilization appears to be regulated by auxin produced in expanding buds and shoots that is transported to bark where it regulates protease gene expression and BSP catabolism.
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Affiliation(s)
- Gen Li
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Rongshoung Lin
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Chioma Egekwu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Joshua Blakeslee
- OARDC Metabolite Analysis Center, Department of Horticulture and Crop Science, The Ohio State University, Wooster, USA
| | - Jinshan Lin
- OARDC Metabolite Analysis Center, Department of Horticulture and Crop Science, The Ohio State University, Wooster, USA
| | - Emily Pettengill
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Angus S Murphy
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Wendy A Peer
- Department of Environmental Science and Technology, University of Maryland, College Park, USA
| | - Nazrul Islam
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
| | - Benjamin A Babst
- College of Forestry, Agriculture and Natural Resources, University of Arkansas at Monticello, Monticello, USA
| | - Fei Gao
- College of Forestry, Agriculture and Natural Resources, University of Arkansas at Monticello, Monticello, USA
| | - Sergey Komarov
- Department of Radiology, Washington University in St. Louis, St. Louis, USA
| | - Yuan-Chuan Tai
- Department of Radiology, Washington University in St. Louis, St. Louis, USA
| | - Gary D Coleman
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, USA
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11
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Tsuchiya M, Giuliani A, Yoshikawa K. Cell-Fate Determination from Embryo to Cancer Development: Genomic Mechanism Elucidated. Int J Mol Sci 2020; 21:E4581. [PMID: 32605138 PMCID: PMC7369777 DOI: 10.3390/ijms21134581] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/12/2020] [Indexed: 12/12/2022] Open
Abstract
Elucidation of the genomic mechanism that guides the cell-fate change is one of the fundamental issues of biology. We previously demonstrated that whole genome expression is coordinated by the emergence of a critical point at both the cell-population and single-cell levels through the physical principle of self-organized criticality. In this paper, we further examine the genomic mechanism that determines the cell-fate changes from embryo to cancer development. The state of the critical point, acting as the organizing center of the cell fate, determines whether the genome resides in a super- or sub-critical state. In the super-critical state, a specific stochastic perturbation can spread over the entire system through the "genome engine", an autonomous critical-control genomic system, whereas in the sub-critical state, the perturbation remains at a local level. The cell-fate changes when the genome becomes super-critical. We provide a consistent framework to develop a time-evolutional transition theory for the biological regulation of the cell-fate change.
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Affiliation(s)
- Masa Tsuchiya
- SEIKO Life Science Laboratory, SRI, Osaka 540-659, Japan
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanitá, 00161 Rome, Italy;
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan;
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12
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McClintick JN, Thapa K, Liu Y, Xuei X, Edenberg HJ. Effects of chronic intermittent ethanol exposure and withdrawal on neuroblastoma cell transcriptome. Alcohol 2020; 85:119-126. [PMID: 31923563 PMCID: PMC7237278 DOI: 10.1016/j.alcohol.2019.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/08/2019] [Accepted: 12/22/2019] [Indexed: 02/06/2023]
Abstract
Cycles of heavy drinking and abstinence can lead to alcohol use disorder. We studied the effects of chronic intermittent ethanol exposure (CIE) over 3 weeks on neuroblastoma cells, using an ethanol concentration frequently attained in binge drinking (40 mM, 184 mg/dL). There were many changes in gene expression but most were small. CIE affected pathways instrumental in the development or plasticity of neurons, including axonal guidance, reelin signaling, and synaptogenesis. Genes involved in dopamine and serotonin signaling were also affected. Changes in transporters and receptors could dampen both NMDA and norepinephrine transmissions. Decreased expression of the GABA transporter SLC6A11 could increase GABA transmission and has been associated with a switch from sweet drinking to ethanol consumption in rats. Ethanol increased stress responses such as the unfolded protein response. TGF-β and NFκB signaling were increased. Most of the genes involved in cholesterol biosynthesis were decreased in expression. Withdrawal for 24 h after CIE caused most of the CIE-induced expression changes to move back toward unexposed levels.
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Affiliation(s)
- Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Kriti Thapa
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Xiaoling Xuei
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.
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13
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Large-Scale Differential Gene Expression Transcriptomic Analysis Identifies a Metabolic Signature Shared by All Cancer Cells. Biomolecules 2020; 10:biom10050701. [PMID: 32365991 PMCID: PMC7277211 DOI: 10.3390/biom10050701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 12/11/2022] Open
Abstract
Cancer-dependent metabolic rewiring is often manifested by selective expression of enzymes essential for the transformed cells’ viability. However, the metabolic variations between normal and transformed cells are not fully characterized, and therefore, a systematic analysis will result in the identification of unknown cellular mechanisms crucial for tumorigenesis. Here, we applied differential gene expression transcriptome analysis to examine the changes in metabolic gene profiles between a wide range of normal tissues and cancer samples. We found that, in contrast to normal tissues which exhibit a tissue-specific expression profile, cancer samples are more homogenous despite their diverse origins. This similarity is due to a “proliferation metabolic signature” (PMS), composed of 158 genes (87 upregulated and 71 downregulated gene sets), where 143 are common to all proliferative cells but 15 are cancer specific. Intriguingly, the PMS gene set is enriched for genes encoding rate-limiting enzymes, and its upregulated set with genes associated with poor patient outcome and essential genes. Among these essential genes is ribulose-5-phosphate-3-epimerase (RPE), which encodes a pentose phosphate pathway enzyme and whose role in cancer is still unclear. Collectively, we identified a set of metabolic genes that can serve as novel cancer biomarkers and potential targets for drug development.
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14
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Alzubaidi A, Tepper J, Lotfi A. A novel deep mining model for effective knowledge discovery from omics data. Artif Intell Med 2020; 104:101821. [DOI: 10.1016/j.artmed.2020.101821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 01/23/2020] [Accepted: 02/17/2020] [Indexed: 10/24/2022]
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15
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Sarmah S, Srivastava R, McClintick JN, Janga SC, Edenberg HJ, Marrs JA. Embryonic ethanol exposure alters expression of sox2 and other early transcripts in zebrafish, producing gastrulation defects. Sci Rep 2020; 10:3951. [PMID: 32127575 PMCID: PMC7054311 DOI: 10.1038/s41598-020-59043-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/21/2020] [Indexed: 01/10/2023] Open
Abstract
Ethanol exposure during prenatal development causes fetal alcohol spectrum disorder (FASD), the most frequent preventable birth defect and neurodevelopmental disability syndrome. The molecular targets of ethanol toxicity during development are poorly understood. Developmental stages surrounding gastrulation are very sensitive to ethanol exposure. To understand the effects of ethanol on early transcripts during embryogenesis, we treated zebrafish embryos with ethanol during pre-gastrulation period and examined the transcripts by Affymetrix GeneChip microarray before gastrulation. We identified 521 significantly dysregulated genes, including 61 transcription factors in ethanol-exposed embryos. Sox2, the key regulator of pluripotency and early development was significantly reduced. Functional annotation analysis showed enrichment in transcription regulation, embryonic axes patterning, and signaling pathways, including Wnt, Notch and retinoic acid. We identified all potential genomic targets of 25 dysregulated transcription factors and compared their interactions with the ethanol-dysregulated genes. This analysis predicted that Sox2 targeted a large number of ethanol-dysregulated genes. A gene regulatory network analysis showed that many of the dysregulated genes are targeted by multiple transcription factors. Injection of sox2 mRNA partially rescued ethanol-induced gene expression, epiboly and gastrulation defects. Additional studies of this ethanol dysregulated network may identify therapeutic targets that coordinately regulate early development.
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Affiliation(s)
- Swapnalee Sarmah
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Rajneesh Srivastava
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sarath C Janga
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - James A Marrs
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA.
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16
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Piper CJM, Rosser EC, Oleinika K, Nistala K, Krausgruber T, Rendeiro AF, Banos A, Drozdov I, Villa M, Thomson S, Xanthou G, Bock C, Stockinger B, Mauri C. Aryl Hydrocarbon Receptor Contributes to the Transcriptional Program of IL-10-Producing Regulatory B Cells. Cell Rep 2019; 29:1878-1892.e7. [PMID: 31722204 PMCID: PMC6856759 DOI: 10.1016/j.celrep.2019.10.018] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/23/2019] [Accepted: 10/03/2019] [Indexed: 12/12/2022] Open
Abstract
Regulatory B cells (Bregs) play a critical role in the control of autoimmunity and inflammation. IL-10 production is the hallmark for the identification of Bregs. However, the molecular determinants that regulate the transcription of IL-10 and control the Breg developmental program remain unknown. Here, we demonstrate that aryl hydrocarbon receptor (AhR) regulates the differentiation and function of IL-10-producing CD19+CD21hiCD24hiBregs and limits their differentiation into B cells that contribute to inflammation. Chromatin profiling and transcriptome analyses show that loss of AhR in B cells reduces expression of IL-10 by skewing the differentiation of CD19+CD21hiCD24hiB cells into a pro-inflammatory program, under Breg-inducing conditions. B cell AhR-deficient mice develop exacerbated arthritis, show significant reductions in IL-10-producing Bregs and regulatory T cells, and show an increase in T helper (Th) 1 and Th17 cells compared with B cell AhR-sufficient mice. Thus, we identify AhR as a relevant contributor to the transcriptional regulation of Breg differentiation.
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Affiliation(s)
- Christopher J M Piper
- Centre for Rheumatology, Division of Medicine, University College London, London, UK
| | - Elizabeth C Rosser
- Centre for Rheumatology, Division of Medicine, University College London, London, UK; University College London Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK; Versus Arthritis Centre for Adolescent Rheumatology at University College London, University College London Hospitals and Great Ormond Street Hospital, London, UK
| | - Kristine Oleinika
- Centre for Rheumatology, Division of Medicine, University College London, London, UK
| | - Kiran Nistala
- Centre for Rheumatology, Division of Medicine, University College London, London, UK
| | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André F Rendeiro
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Aggelos Banos
- Laboratory of Inflammation and Autoimmunity, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | | | - Matteo Villa
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Scott Thomson
- Centre for Rheumatology, Division of Medicine, University College London, London, UK
| | - Georgina Xanthou
- Cellular Immunology Lab, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria; Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | | | - Claudia Mauri
- Centre for Rheumatology, Division of Medicine, University College London, London, UK.
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17
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Moi L, Braaten T, Al-Shibli K, Lund E, Busund LTR. Differential expression of the miR-17-92 cluster and miR-17 family in breast cancer according to tumor type; results from the Norwegian Women and Cancer (NOWAC) study. J Transl Med 2019; 17:334. [PMID: 31581940 PMCID: PMC6775665 DOI: 10.1186/s12967-019-2086-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 09/24/2019] [Indexed: 12/21/2022] Open
Abstract
Background MicroRNAs (miRNAs) are promising biomarkers due to their structural stability and distinct expression profile in various cancers. We wanted to explore the miRNA expression in benign breast tissue and breast cancer subgroups in the Norwegian Women and Cancer study. Methods Specimens and histopathological data from study participants in Northern Norway diagnosed with breast cancer, and benign tissue from breast reduction surgery were collected. Main molecular subtypes were based on surrogate markers; luminal A (ER+ and/or PR+, HER2− and Ki67 ≤ 30%), luminal B (ER+ and/or PR+, HER2− and Ki67 > 30% or ER+ and/or PR+ and HER2+), HER2 positive (ER− and PR− and HER2+) and triple-negative (ER−, PR− and HER2−). RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue, and miRNAs were successfully analyzed in 102 cancers and 36 benign controls using the 7th generation miRCURY LNA microarray containing probes targeting all human miRNAs as annotated in miRBASE version 19.0. Validation with RT-qPCR was performed. Results On average, 450 miRNAs were detected in each sample, and 304 miRNAs were significantly different between malignant and benign tissue. Subgroup analyses of cancer cases revealed 23 miRNAs significantly different between ER+ and ER− tumors, and 47 miRNAs different between tumors stratified according to grade. Significantly higher levels were found in high grade tumors for miR-17-5p (p = 0.006), miR-20a-5p (p = 0.007), miR-106b-5p (p = 0.007), miR-93-5p (p = 0.007) and miR-25-3p (p = 0.015) from the paralogous clusters miR-17-92 and miR-106b-25. Expression of miR-17-5p (p = 0.0029), miR-20a-5p (p = 0.0021), miR-92a-3p (p = 0.011) and miR-106b-5p (p = 0.021) was significantly higher in triple-negative tumors compared to the rest, and miR-17-5p and miR-20a-5p were significantly lower in luminal A tumors. Conclusions miRNA expression profiles were significantly different between malignant and benign tissue and between cancer subgroups according to ER− status, grade and molecular subtype. miRNAs in the miR-17-92 cluster and miR-17 family were overexpressed in high grade and triple-negative tumors associated with aggressive behavior. The expression and functional role of these miRNAs should be further studied in breast cancer to explore their potential as biomarkers in diagnostic pathology and clinical oncology.
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Affiliation(s)
- Line Moi
- Institute of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway. .,Department of Clinical Pathology, University Hospital of North Norway, Tromsø, Norway.
| | - Tonje Braaten
- Institute of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway
| | - Khalid Al-Shibli
- Institute of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway.,Department of Pathology, Nordland Hospital, Bodø, Norway
| | - Eiliv Lund
- Institute of Community Medicine, UiT The Arctic University of Norway, Tromsø, Norway.,Cancer Registry of Norway, Oslo, Norway
| | - Lill-Tove Rasmussen Busund
- Institute of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway.,Department of Clinical Pathology, University Hospital of North Norway, Tromsø, Norway
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18
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Identification of Alternatively-Activated Pathways between Primary Breast Cancer and Liver Metastatic Cancer Using Microarray Data. Genes (Basel) 2019; 10:genes10100753. [PMID: 31557971 PMCID: PMC6826985 DOI: 10.3390/genes10100753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 12/19/2022] Open
Abstract
Alternatively-activated pathways have been observed in biological experiments in cancer studies, but the concept had not been fully explored in computational cancer system biology. Therefore, an alternatively-activated pathway identification method was proposed and applied to primary breast cancer and breast cancer liver metastasis research using microarray data. Interestingly, the results show that cytokine-cytokine receptor interaction and calcium signaling were significantly enriched under both conditions. TGF beta signaling was found to be the hub in network topology analysis. In total, three types of alternatively-activated pathways were recognized. In the cytokine-cytokine receptor interaction pathway, four active alteration patterns in gene pairs were noticed. Thirteen cytokine-cytokine receptor pairs with inverse activity changes of both genes were verified by the literature. The second type was that some sub-pathways were active under only one condition. For the third type, nodes were significantly active in both conditions, but with different active genes. In the calcium signaling and TGF beta signaling pathways, node E2F5 and E2F4 were significantly active in primary breast cancer and metastasis, respectively. Overall, our study demonstrated the first time using microarray data to identify alternatively-activated pathways in breast cancer liver metastasis. The results showed that the proposed method was valid and effective, which could be helpful for future research for understanding the mechanism of breast cancer metastasis.
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19
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Abnormal axon guidance signals and reduced interhemispheric connection via anterior commissure in neonates of marmoset ASD model. Neuroimage 2019; 195:243-251. [DOI: 10.1016/j.neuroimage.2019.04.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 03/18/2019] [Accepted: 04/02/2019] [Indexed: 12/18/2022] Open
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20
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Siangphoe U, Archer KJ, Mukhopadhyay ND. Classical and Bayesian random-effects meta-analysis models with sample quality weights in gene expression studies. BMC Bioinformatics 2019; 20:18. [PMID: 30626315 PMCID: PMC6327440 DOI: 10.1186/s12859-018-2491-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/12/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Random-effects (RE) models are commonly applied to account for heterogeneity in effect sizes in gene expression meta-analysis. The degree of heterogeneity may differ due to inconsistencies in sample quality. High heterogeneity can arise in meta-analyses containing poor quality samples. We applied sample-quality weights to adjust the study heterogeneity in the DerSimonian and Laird (DSL) and two-step DSL (DSLR2) RE models and the Bayesian random-effects (BRE) models with unweighted and weighted data, Gibbs and Metropolis-Hasting (MH) sampling algorithms, weighted common effect, and weighted between-study variance. We evaluated the performance of the models through simulations and illustrated application of the methods using Alzheimer's gene expression datasets. RESULTS Sample quality adjusting within study variance (wP6) models provided an appropriate reduction of differentially expressed (DE) genes compared to other weighted functions in classical RE models. The BRE model with a uniform(0,1) prior was appropriate for detecting DE genes as compared to the models with other prior distributions. The precision of DE gene detection in the heterogeneous data was increased with the DSLR2wP6 weighted model compared to the DSLwP6 weighted model. Among the BRE weighted models, the wP6weighted- and unweighted-data models and both Gibbs- and MH-based models performed similarly. The wP6 weighted common-effect model performed similarly to the unweighted model in the homogeneous data, but performed worse in the heterogeneous data. The wP6weighted data were appropriate for detecting DE genes with high precision, while the wP6weighted between-study variance models were appropriate for detecting DE genes with high overall accuracy. Without the weight, when the number of genes in microarray increased, the DSLR2 performed stably, while the overall accuracy of the BRE model was reduced. When applying the weighted models in the Alzheimer's gene expression data, the number of DE genes decreased in all metadata sets with the DSLR2wP6weighted and the wP6weighted between study variance models. Four hundred and forty-six DE genes identified by the wP6weighted between study variance model could be potentially down-regulated genes that may contribute to good classification of Alzheimer's samples. CONCLUSIONS The application of sample quality weights can increase precision and accuracy of the classical RE and BRE models; however, the performance of the models varied depending on data features, levels of sample quality, and adjustment of parameter estimates.
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Affiliation(s)
- Uma Siangphoe
- Office of Biostatistics, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland USA
| | - Kellie J. Archer
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio USA
| | - Nitai D. Mukhopadhyay
- Department of Biostatistics, Virginia Commonwealth University, Richmond, Virginia USA
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21
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Jividen K, Kedzierska KZ, Yang CS, Szlachta K, Ratan A, Paschal BM. Genomic analysis of DNA repair genes and androgen signaling in prostate cancer. BMC Cancer 2018; 18:960. [PMID: 30305041 PMCID: PMC6180441 DOI: 10.1186/s12885-018-4848-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/21/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The cellular effects of androgen are transduced through the androgen receptor, which controls the expression of genes that regulate biosynthetic processes, cell growth, and metabolism. Androgen signaling also impacts DNA damage signaling through mechanisms involving gene expression and transcription-associated DNA damaging events. Defining the contributions of androgen signaling to DNA repair is important for understanding androgen receptor function, and it also has translational implications. METHODS We generated RNA-seq data from multiple prostate cancer lines and used bioinformatic analyses to characterize androgen-regulated gene expression. We compared the results from cell lines with gene expression data from prostate cancer xenografts, and patient samples, to query how androgen signaling and prostate cancer progression influences the expression of DNA repair genes. We performed whole genome sequencing to help characterize the status of the DNA repair machinery in widely used prostate cancer lines. Finally, we tested a DNA repair enzyme inhibitor for effects on androgen-dependent transcription. RESULTS Our data indicates that androgen signaling regulates a subset of DNA repair genes that are largely specific to the respective model system and disease state. We identified deleterious mutations in the DNA repair genes RAD50 and CHEK2. We found that inhibition of the DNA repair enzyme MRE11 with the small molecule mirin inhibits androgen-dependent transcription and growth of prostate cancer cells. CONCLUSIONS Our data supports the view that crosstalk between androgen signaling and DNA repair occurs at multiple levels, and that DNA repair enzymes in addition to PARPs, could be actionable targets in prostate cancer.
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Affiliation(s)
- Kasey Jividen
- Center for Cell Signaling, University of Virginia, Charlottesville, VA USA
| | | | - Chun-Song Yang
- Center for Cell Signaling, University of Virginia, Charlottesville, VA USA
| | - Karol Szlachta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA USA
| | - Bryce M Paschal
- Center for Cell Signaling, University of Virginia, Charlottesville, VA USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA USA
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22
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Vural S, Simon R, Krushkal J. Correlation of gene expression and associated mutation profiles of APOBEC3A, APOBEC3B, REV1, UNG, and FHIT with chemosensitivity of cancer cell lines to drug treatment. Hum Genomics 2018; 12:20. [PMID: 29642934 PMCID: PMC5896091 DOI: 10.1186/s40246-018-0150-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/23/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The APOBEC gene family of cytidine deaminases plays important roles in DNA repair and mRNA editing. In many cancers, APOBEC3B increases the mutation load, generating clusters of closely spaced, single-strand-specific DNA substitutions with a characteristic hypermutation signature. Some studies also suggested a possible involvement of APOBEC3A, REV1, UNG, and FHIT in molecular processes affecting APOBEC mutagenesis. It is important to understand how mutagenic processes linked to the activity of these genes may affect sensitivity of cancer cells to treatment. RESULTS We used information from the Cancer Cell Line Encyclopedia and the Genomics of Drug Sensitivity in Cancer resources to examine associations of the prevalence of APOBEC-like motifs and mutational loads with expression of APOBEC3A, APOBEC3B, REV1, UNG, and FHIT and with cell line chemosensitivity to 255 antitumor drugs. Among the five genes, APOBEC3B expression levels were bimodally distributed, whereas expression of APOBEC3A, REV1, UNG, and FHIT was unimodally distributed. The majority of the cell lines had low levels of APOBEC3A expression. The strongest correlations of gene expression levels with mutational loads or with measures of prevalence of APOBEC-like motif counts and kataegis clusters were observed for REV1, UNG, and APOBEC3A. Sensitivity or resistance of cell lines to JQ1, palbociclib, bicalutamide, 17-AAG, TAE684, MEK inhibitors refametinib, PD-0325901, and trametinib and a number of other agents was correlated with candidate gene expression levels or with abundance of APOBEC-like motif clusters in specific cancers or across cancer types. CONCLUSIONS We observed correlations of expression levels of the five candidate genes in cell line models with sensitivity to cancer drug treatment. We also noted suggestive correlations between measures of abundance of APOBEC-like sequence motifs with drug sensitivity in small samples of cell lines from individual cancer categories, which require further validation in larger datasets. Molecular mechanisms underlying the links between the activities of the products of each of the five genes, the resulting mutagenic processes, and sensitivity to each category of antitumor agents require further investigation.
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Affiliation(s)
- Suleyman Vural
- Computational and Systems Biology Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD 20850 USA
| | - Richard Simon
- Computational and Systems Biology Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD 20850 USA
| | - Julia Krushkal
- Computational and Systems Biology Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr, Rockville, MD 20850 USA
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23
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Hato T, Zollman A, Plotkin Z, El-Achkar TM, Maier BF, Pay SL, Dube S, Cabral P, Yoshimoto M, McClintick J, Dagher PC. Endotoxin Preconditioning Reprograms S1 Tubules and Macrophages to Protect the Kidney. J Am Soc Nephrol 2017; 29:104-117. [PMID: 29018138 DOI: 10.1681/asn.2017060624] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/14/2017] [Indexed: 12/21/2022] Open
Abstract
Preconditioning with a low dose of endotoxin confers unparalleled protection against otherwise lethal models of sepsis. The mechanisms of preconditioning have been investigated extensively in isolated immune cells such as macrophages. However, the role of tissue in mediating the protective response generated by preconditioning remains unknown. Here, using the kidney as a model organ, we investigated cell type-specific responses to preconditioning. Compared with preadministration of vehicle, endotoxin preconditioning in the cecal ligation and puncture mouse model of sepsis led to significantly enhanced survival and reduced bacterial load in several organs. Furthermore, endotoxin preconditioning reduced serum levels of proinflammatory cytokines, upregulated molecular pathways involved in phagocytosis, and prevented the renal function decline and injury induced in mice by a toxic dose of endotoxin. The protective phenotype involved the clustering of macrophages around S1 segments of proximal tubules, and full renal protection required both macrophages and renal tubular cells. Using unbiased S1 transcriptomic and tissue metabolomic approaches, we identified multiple protective molecules that were operative in preconditioned animals, including molecules involved in antibacterial defense, redox balance, and tissue healing. We conclude that preconditioning reprograms macrophages and tubules to generate a protective environment, in which tissue health is preserved and immunity is controlled yet effective. Endotoxin preconditioning can thus be used as a discovery platform, and understanding the role and participation of both tissue and macrophages will help refine targeted therapies for sepsis.
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Affiliation(s)
| | | | | | - Tarek M El-Achkar
- Departments of Medicine and.,Cellular and Integrative Physiology, Indiana University, Indianapolis, Indiana.,Roudebush Indianapolis Veterans Affairs Medical Center, Indianapolis, Indiana
| | | | | | - Shataakshi Dube
- Department of Neurobiology, Duke University Medical School, Durham, North Carolina
| | - Pablo Cabral
- Miromatrix Medical Inc., Eden Prairie, Minnesota; and
| | - Momoko Yoshimoto
- Institute of Molecular Medicine, Center for Stem Cell Research and Regenerative Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | | | - Pierre C Dagher
- Departments of Medicine and .,Cellular and Integrative Physiology, Indiana University, Indianapolis, Indiana.,Roudebush Indianapolis Veterans Affairs Medical Center, Indianapolis, Indiana
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24
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Johnson CM, Subramanian A, Pattathil S, Correll MJ, Kiss JZ. Comparative transcriptomics indicate changes in cell wall organization and stress response in seedlings during spaceflight. AMERICAN JOURNAL OF BOTANY 2017; 104:1219-1231. [PMID: 28827451 PMCID: PMC5821596 DOI: 10.3732/ajb.1700079] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/16/2017] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Plants will play an important role in the future of space exploration as part of bioregenerative life support. Thus, it is important to understand the effects of microgravity and spaceflight on gene expression in plant development. METHODS We analyzed the transcriptome of Arabidopsis thaliana using the Biological Research in Canisters (BRIC) hardware during Space Shuttle mission STS-131. The bioinformatics methods used included RMA (robust multi-array average), MAS5 (Microarray Suite 5.0), and PLIER (probe logarithmic intensity error estimation). Glycome profiling was used to analyze cell wall composition in the samples. In addition, our results were compared to those of two other groups using the same hardware on the same mission (BRIC-16). KEY RESULTS In our BRIC-16 experiments, we noted expression changes in genes involved in hypoxia and heat shock responses, DNA repair, and cell wall structure between spaceflight samples compared to the ground controls. In addition, glycome profiling supported our expression analyses in that there was a difference in cell wall components between ground control and spaceflight-grown plants. Comparing our studies to those of the other BRIC-16 experiments demonstrated that, even with the same hardware and similar biological materials, differences in results in gene expression were found among these spaceflight experiments. CONCLUSIONS A common theme from our BRIC-16 space experiments and those of the other two groups was the downregulation of water stress response genes in spaceflight. In addition, all three studies found differential regulation of genes associated with cell wall remodeling and stress responses between spaceflight-grown and ground control plants.
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Affiliation(s)
- Christina M. Johnson
- Miami University, Department of Biology 212 Pearson Hall, Oxford, Ohio 45056 USA
| | - Aswati Subramanian
- Miami University, Department of Biology 212 Pearson Hall, Oxford, Ohio 45056 USA
| | - Sivakumar Pattathil
- University of Georgia Complex Carbohydrate Research Center, 315 Riverbend Road, Athens, Georgia 30602 USA
- Mascoma, LLC (Lallemand Inc.) 67 Etna Road Lebanon, New Hampshire 03766 USA
| | - Melanie J. Correll
- University of Florida, Department of Agricultural and Biological Engineering 209 Frazier Rogers Hall, Gainesville, Florida 32611 USA
| | - John Z. Kiss
- University of North Carolina at Greensboro, Department of Biology, Greensboro, North Carolina 27412 USA
- Author for correspondence ()
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25
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Zou YF, Wen D, Zhao Q, Shen PY, Shi H, Zhao Q, Chen YX, Zhang W. Urinary MicroRNA-30c-5p and MicroRNA-192-5p as potential biomarkers of ischemia-reperfusion-induced kidney injury. Exp Biol Med (Maywood) 2017; 242:657-667. [PMID: 28056546 DOI: 10.1177/1535370216685005] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Early detection of acute kidney injury is difficult due to lack of known biomarkers; previous studies have tried to identify new biomarkers for detecting acute kidney injury at an early stage. MicroRNA, a 21-23 nucleotide noncoding RNA molecule, has emerged as a desirable marker in the diagnosis and prognosis of various diseases. This study aims to identify the expression profile of microRNA in ischemia-reperfusion-induced kidney injury and determine the possibility of using the candidate microRNA as biomarker for the detection of I/R-induced kidney injury. Based on the established rat model of I/R-induced kidney injury, a microarray analysis of rat urine was performed at the beginning of operation (0 h) as well as 72 h post operation. To validate the results, urine samples from 71 patients who underwent cardiac surgery were collected, after which urinalysis was conducted to determine the microRNA concentration. An alternative expression profile of microRNAs was detected in rat urine. The quantitative validation of microRNA showed that the expression of miR-30c-5p, miR-192-5p, and miR-378a-3p was elevated significantly in urine post operation, which was consistent with those of the microarray analysis and earlier than kidney injury molecule-1 (KIM-1). In patients with acute kidney injury, increased levels of miR-30c-5p and miR-192-5p were also detected 2 h post operation, and miR-30c-5p showed preferable diagnostic value compared with protein-based biomarkers. In conclusion, an aberrant expression profile of microRNA was detected in rat urine based on the established ischemia-reperfusion animal model. Both miR-30c-5p and miR-192-5p served as important potential diagnostic markers for I/R-induced kidney injury. Impact statement Firstly, one differentiating factor in our study is that the candidate miRNAs were screened in a controlled animal model rather than in patients with acute kidney injury (AKI) to ensure the purity of the cause of disease and to avoid possible effects of comorbidities on the spectrum of urine miRNA. This ensured the presence of only the relevant candidate miRNA (that associated with I/R injury); and what's more, the alterative expression of miR-192-5p and miR-30c-5p in animal model, patients with AKI, and cell model was confirmed simultaneously, which is likely to be more convincing. Secondly, the candidate miRNAs were screened sequentially at regular time points, which covered the initiation, progression, and partial repair stages, thus ensuring that no significant miRNAs were omitted in the screening process, and miR-biomarkers in 2 h post operation showed preferable diagnostic performance.
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Affiliation(s)
- Yan-Fang Zou
- 1 Department of Nephrology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, PR China
| | - Dan Wen
- 1 Department of Nephrology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, PR China
| | - Qian Zhao
- 2 Key Laboratory of Cell Differentiation and Apoptosis of National Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, PR China
| | - Ping-Yan Shen
- 1 Department of Nephrology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, PR China
| | - Hao Shi
- 1 Department of Nephrology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, PR China
| | - Qiang Zhao
- 3 Cardiovascular Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, PR China Yan-Fang Zou and Dan Wen contributed equally to this work
| | - Yong-Xi Chen
- 1 Department of Nephrology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, PR China
| | - Wen Zhang
- 1 Department of Nephrology, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, PR China
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26
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Herring BP, Hoggatt AM, Griffith SL, McClintick JN, Gallagher PJ. Inflammation and vascular smooth muscle cell dedifferentiation following carotid artery ligation. Physiol Genomics 2016; 49:115-126. [PMID: 28039430 PMCID: PMC5374455 DOI: 10.1152/physiolgenomics.00095.2016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/21/2016] [Accepted: 12/21/2016] [Indexed: 11/22/2022] Open
Abstract
Following vascular injury medial smooth muscle cells dedifferentiate and migrate through the internal elastic lamina where they form a neointima. The goal of the current study was to identify changes in gene expression that occur before the development of neointima and are associated with the early response to injury. Vascular injury was induced in C57BL/6 mice and in Myh11-creER(T2) mTmG reporter mice by complete ligation of the left carotid artery. Reporter mice were used to visualize cellular changes in the injured vessels. Total RNA was isolated from control carotid arteries or from carotid arteries 3 days following ligation of C57BL/6 mice and analyzed by Affymetrix microarray and quantitative RT-PCR. This analysis revealed decreased expression of mRNAs encoding smooth muscle-specific contractile proteins that was accompanied by a marked increase in a host of mRNAs encoding inflammatory cytokines following injury. There was also marked decrease in molecules associated with BMP, Wnt, and Hedgehog signaling and an increase in those associated with B cell, T cell, and macrophage signaling. Expression of a number of noncoding RNAs were also altered following injury with microRNAs 143/145 being dramatically downregulated and microRNAs 1949 and 142 upregulated. Several long noncoding RNAs showed altered expression that mirrored the expression of their nearest coding genes. These data demonstrate that following carotid artery ligation an inflammatory cascade is initiated that is associated with the downregulation of coding and noncoding RNAs that are normally required to maintain smooth muscle cells in a differentiated state.
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Affiliation(s)
- B Paul Herring
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana; and
| | - April M Hoggatt
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana; and
| | - Sarah L Griffith
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana; and
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Patricia J Gallagher
- Department of Cellular and Integrative Physiology, Indiana University School of Medicine, Indianapolis, Indiana; and
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27
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Tsuchiya M, Giuliani A, Hashimoto M, Erenpreisa J, Yoshikawa K. Self-Organizing Global Gene Expression Regulated through Criticality: Mechanism of the Cell-Fate Change. PLoS One 2016; 11:e0167912. [PMID: 27997556 PMCID: PMC5173342 DOI: 10.1371/journal.pone.0167912] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/22/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND A fundamental issue in bioscience is to understand the mechanism that underlies the dynamic control of genome-wide expression through the complex temporal-spatial self-organization of the genome to regulate the change in cell fate. We address this issue by elucidating a physically motivated mechanism of self-organization. PRINCIPAL FINDINGS Building upon transcriptome experimental data for seven distinct cell fates, including early embryonic development, we demonstrate that self-organized criticality (SOC) plays an essential role in the dynamic control of global gene expression regulation at both the population and single-cell levels. The novel findings are as follows: i) Mechanism of cell-fate changes: A sandpile-type critical transition self-organizes overall expression into a few transcription response domains (critical states). A cell-fate change occurs by means of a dissipative pulse-like global perturbation in self-organization through the erasure of initial-state critical behaviors (criticality). Most notably, the reprogramming of early embryo cells destroys the zygote SOC control to initiate self-organization in the new embryonal genome, which passes through a stochastic overall expression pattern. ii) Mechanism of perturbation of SOC controls: Global perturbations in self-organization involve the temporal regulation of critical states. Quantitative evaluation of this perturbation in terminal cell fates reveals that dynamic interactions between critical states determine the critical-state coherent regulation. The occurrence of a temporal change in criticality perturbs this between-states interaction, which directly affects the entire genomic system. Surprisingly, a sub-critical state, corresponding to an ensemble of genes that shows only marginal changes in expression and consequently are considered to be devoid of any interest, plays an essential role in generating a global perturbation in self-organization directed toward the cell-fate change. CONCLUSION AND SIGNIFICANCE 'Whole-genome' regulation of gene expression through self-regulatory SOC control complements gene-by-gene fine tuning and represents a still largely unexplored non-equilibrium statistical mechanism that is responsible for the massive reprogramming of genome expression.
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Affiliation(s)
- Masa Tsuchiya
- Systems Biology Program, School of Media and Governance, Keio University, Fujisawa, Japan
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanitá, Rome, Italy
| | - Midori Hashimoto
- Graduate School of Frontier Science, the University of Tokyo, Kashiwa, Japan
| | | | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
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28
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Riva N, Clarelli F, Domi T, Cerri F, Gallia F, Trimarco A, Brambilla P, Lunetta C, Lazzerini A, Lauria G, Taveggia C, Iannaccone S, Nobile-Orazio E, Comi G, D’Antonio M, Martinelli-Boneschi F, Quattrini A. Unraveling gene expression profiles in peripheral motor nerve from amyotrophic lateral sclerosis patients: insights into pathogenesis. Sci Rep 2016; 6:39297. [PMID: 27982123 PMCID: PMC5159906 DOI: 10.1038/srep39297] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 11/21/2016] [Indexed: 01/12/2023] Open
Abstract
The aim of the present study is to investigate the molecular pathways underlying amyotrophic lateral sclerosis (ALS) pathogenesis within the peripheral nervous system. We analyzed gene expression changes in human motor nerve diagnostic biopsies obtained from eight ALS patients and seven patients affected by motor neuropathy as controls. An integrated transcriptomics and system biology approach was employed. We identified alterations in the expression of 815 genes, with 529 up-regulated and 286 down-regulated in ALS patients. Up-regulated genes clustered around biological process involving RNA processing and protein metabolisms. We observed a significant enrichment of up-regulated small nucleolar RNA transcripts (p = 2.68*10-11) and genes related to endoplasmic reticulum unfolded protein response and chaperone activity. We found a significant down-regulation in ALS of genes related to the glutamate metabolism. Interestingly, a network analysis highlighted HDAC2, belonging to the histone deacetylase family, as the most interacting node. While so far gene expression studies in human ALS have been performed in postmortem tissues, here specimens were obtained from biopsy at an early phase of the disease, making these results new in the field of ALS research and therefore appealing for gene discovery studies.
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Affiliation(s)
- Nilo Riva
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Ferdinando Clarelli
- Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Teuta Domi
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Federica Cerri
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Gallia
- 2Neurology, IRCCS Istituto Clinico Humanitas, Milano University, Milan, Italy
| | - Amelia Trimarco
- Axo-glia interactions Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Paola Brambilla
- Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Christian Lunetta
- NEuroMuscular Omnicentre (NEMO), Niguarda Ca Granda Hospital, Milan, Italy
| | - Alberto Lazzerini
- Hand Surgery and Microsurgery Unit, IRCCS Humanitas Clinical Institute, Milan, Italy
| | - Giuseppe Lauria
- 3rd Neurology Unit, IRCCS Foundation “Carlo Besta” Neurological Institute, Milan, Italy
| | - Carla Taveggia
- Axo-glia interactions Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Sandro Iannaccone
- Department of Clinical Neurosciences, San Raffaele Scientific Institute, Milan, Italy
| | | | - Giancarlo Comi
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
- Universita` Vita e Salute San Raffaele, Milan, Italy
| | - Maurizio D’Antonio
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Filippo Martinelli-Boneschi
- Laboratory of Genetics of Complex Neurological Disorders, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Angelo Quattrini
- Experimental Neuropathology Unit, Institute of Experimental Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
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29
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Friedrich J, Brand B, Graunke KL, Langbein J, Schwerin M, Ponsuksili S. Adrenocortical Expression Profiling of Cattle with Distinct Juvenile Temperament Types. Behav Genet 2016; 47:102-113. [PMID: 27586633 DOI: 10.1007/s10519-016-9816-0] [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] [Received: 12/18/2015] [Accepted: 08/27/2016] [Indexed: 01/13/2023]
Abstract
Temperament affects ease of handling, animal welfare, and economically important production traits in cattle. The use of gene expression profiles as molecular traits provides a novel means of gaining insight into behavioural genetics. In this study, differences in adrenocortical expression profiles between 60 F2 cows (Charolais × German Holstein) of distinct temperament types were analysed. The cows were assessed in a novel-human test at an age of 90 days. Most of the adrenal cortex transcripts which were differentially expressed (FDR <0.05) were found between temperament types of 'fearful/neophobic-alert' and all other temperament types. These transcripts belong to several biological functions like NRF2-mediated oxidative stress response, Glucocorticoid Receptor Signalling and Complement System. Overall, the present study provides new insight into transcriptional differences in the adrenal cortex between cows of distinct temperament types. Genetic regulations of such molecular traits facilitate uncovering positional and functional gene candidates for temperament type in cattle.
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Affiliation(s)
- Juliane Friedrich
- Institute for Farm Animal Research and Technology, University of Rostock, Rostock, Germany
| | - Bodo Brand
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Katharina Luise Graunke
- Institute for Behavioural Physiology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Jan Langbein
- Institute for Behavioural Physiology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Manfred Schwerin
- Institute for Farm Animal Research and Technology, University of Rostock, Rostock, Germany.,Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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30
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Viger M, Smith HK, Cohen D, Dewoody J, Trewin H, Steenackers M, Bastien C, Taylor G. Adaptive mechanisms and genomic plasticity for drought tolerance identified in European black poplar (Populus nigra L.). TREE PHYSIOLOGY 2016; 36:909-28. [PMID: 27174702 PMCID: PMC4969554 DOI: 10.1093/treephys/tpw017] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/14/2016] [Indexed: 05/17/2023]
Abstract
Summer droughts are likely to increase in frequency and intensity across Europe, yet long-lived trees may have a limited ability to tolerate drought. It is therefore critical that we improve our understanding of phenotypic plasticity to drought in natural populations for ecologically and economically important trees such as Populus nigra L. A common garden experiment was conducted using ∼500 wild P. nigra trees, collected from 11 river populations across Europe. Phenotypic variation was found across the collection, with southern genotypes from Spain and France characterized by small leaves and limited biomass production. To examine the relationship between phenotypic variation and drought tolerance, six genotypes with contrasting leaf morphologies were subjected to a water deficit experiment. 'North eastern' genotypes were collected at wet sites and responded to water deficit with reduced biomass growth, slow stomatal closure and reduced water use efficiency (WUE) assessed by Δ(13)C. In contrast, 'southern' genotypes originating from arid sites showed rapid stomatal closure, improved WUE and limited leaf loss. Transcriptome analyses of a genotype from Spain (Sp2, originating from an arid site) and another from northern Italy (Ita, originating from a wet site) revealed dramatic differences in gene expression response to water deficit. Transcripts controlling leaf development and stomatal patterning, including SPCH, ANT, ER, AS1, AS2, PHB, CLV1, ERL1-3 and TMM, were down-regulated in Ita but not in Sp2 in response to drought.
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Affiliation(s)
- Maud Viger
- Centre for Biological Sciences, University of Southampton, Life Sciences Building, Southampton SO17 1BJ, UK
| | - Hazel K Smith
- Centre for Biological Sciences, University of Southampton, Life Sciences Building, Southampton SO17 1BJ, UK
| | - David Cohen
- UMR Ecologie et Ecophysiologie Forestières, INRA NANCY-Lorraine, 54280 Champenoux, France UMR Ecologie et Ecophysiologie Forestière, Université de Lorraine, BP 239, F-54506 Vandoeuvre, France
| | - Jennifer Dewoody
- Centre for Biological Sciences, University of Southampton, Life Sciences Building, Southampton SO17 1BJ, UK Present address: USDA Forest Service, National Forest Genetics Lab, 2480 Carson Road, Placerville, CA 95667, USA
| | - Harriet Trewin
- Centre for Biological Sciences, University of Southampton, Life Sciences Building, Southampton SO17 1BJ, UK
| | - Marijke Steenackers
- Ministry of the Flemish Community, Research Institute for Nature and Forest (INBO), Geraardsbergen B-9500, Belgium
| | - Catherine Bastien
- INRA, Unité de Recherche Amélioration Génétique et Physiologie Forestières, 2163 avenue de la Pomme de Pin, CS 40001 Ardon, 45075 Orléans Cedex 2, France
| | - Gail Taylor
- Centre for Biological Sciences, University of Southampton, Life Sciences Building, Southampton SO17 1BJ, UK
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31
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Anand A, McClintick JN, Murrell J, Karne H, Nurnberger JI, Edenberg HJ. Effects of Lithium Monotherapy for Bipolar Disorder on Gene Expression in Peripheral Lymphocytes. MOLECULAR NEUROPSYCHIATRY 2016; 2:115-123. [PMID: 27867936 DOI: 10.1159/000446348] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/20/2016] [Indexed: 11/19/2022]
Abstract
BACKGROUND This study investigated the effect of lithium monotherapy on peripheral lymphocyte gene expression in bipolar disorder (BD). METHOD Twenty-two medication-free bipolar subjects (11 hypomanic, 11 depressed) were started on lithium monotherapy. Closely matched healthy subjects (n = 15) were included as controls but did not receive treatment. Blood RNA samples were collected at baseline and after 2 and 8 weeks of treatment. RNA expression was measured using the Affymetrix GeneChip® Human Gene 1.0 ST Array followed by Ingenuity pathways analysis. The results for the contrast of weeks 2 and 8 were not significantly different and were combined. RESULTS In BD subjects, 56 genes showed significant (false discovery rate <0.1) expression changes from baseline; the effect sizes and directions for all of these were similar at weeks 2 and 8. Among these were immune-related genes (IL5RA, MOK, IFI6, and RFX2), purinergic receptors (P2RY14, P2RY2, and ADORA3) and signal transduction-related genes (CAMK1 and PIK3R6). Pathway and upstream regulator analysis also revealed that lithium altered several immune- and signal transduction-related functions. Differentially expressed genes did not correlate with week 8 clinical response, but other genes involved in protein synthesis and degradation did. CONCLUSION Peripheral gene expression may serve as a biomarker of lithium effect.
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Affiliation(s)
- Amit Anand
- Center for Behavioral Health, Cleveland Clinic, Cleveland, Ohio, USA; Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Ind., USA
| | - Jeanette N McClintick
- Department of Biochemistry and Molecular Biology and Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, Ind., USA
| | - Jill Murrell
- Department of Biochemistry and Molecular Biology and Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, Ind., USA
| | - Harish Karne
- Center for Behavioral Health, Cleveland Clinic, Cleveland, Ohio, USA; Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Ind., USA
| | - John I Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Ind., USA
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology and Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, Ind., USA
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32
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Yu C, Wales SQ, Mammel MK, Hida K, Kulka M. Optimizing a custom tiling microarray for low input detection and identification of unamplified virus targets. J Virol Methods 2016; 234:54-64. [PMID: 27033182 DOI: 10.1016/j.jviromet.2016.03.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 03/04/2016] [Accepted: 03/14/2016] [Indexed: 12/31/2022]
Abstract
Viruses are major pathogens causing foodborne illnesses and are often present at low levels in foods, thus requiring sensitive techniques for their detection in contaminated foods. The lack of efficient culture methods for many foodborne viruses and the potential for multi-species viral contamination have driven investigation toward non-amplification based methods for virus detection and identification. A custom DNA microarray (FDA_EVIR) was assessed for its sensitivity in the detection and identification of low-input virus targets, human hepatitis A virus, norovirus, and coxsackievirus, individually and in combination. Modifications to sample processing were made to accommodate low input levels of unamplified virus targets, which included addition of carrier cDNA, RNase treatment, and optimization of DNase I-mediated target fragmentation. Amplification-free detection and identification of foodborne viruses were achieved in the range of 250-500 copies of virus RNA. Alternative data analysis methods were employed to distinguish the genotypes of the viruses particularly at lower levels of target input and the single probe-based analysis approach made it possible to identify a minority species in a multi-virus complex. The oligonucleotide array is shown to be a promising platform to detect foodborne viruses at low levels close to what are anticipated in food or environmental samples.
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Affiliation(s)
- Christine Yu
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA
| | - Samantha Q Wales
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA
| | - Mark K Mammel
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA
| | - Kaoru Hida
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA
| | - Michael Kulka
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 20708, USA.
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Gene Expression in HIV-Associated Neurocognitive Disorders: A Meta-Analysis. J Acquir Immune Defic Syndr 2016; 70:479-88. [PMID: 26569176 DOI: 10.1097/qai.0000000000000800] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
OBJECTIVES To identify differentially expressed (DE) genes in HIV-associated neurocognitive disorders (HAND) patients in comparison with HIV-infected patients without HAND and controls. DESIGN A meta-analysis of publicly available gene expression data from HIV postmortem brain tissue studies. METHODS We selected studies using clearly defined inclusion and exclusion criteria. Within study data preprocessing and individual analyses were performed for each brain region. The following meta-analytic methods were applied: combining P values, combining effect sizes with and without a permutation method. The DE genes were defined with a false discovery rate less than 5% using Benjamini-Hochberg method. RESULTS Our meta-analysis on 3 studies encompasses analyses of over 48 postmortem brains [25 HAND, 7 HIV encephalitis (HIVE), 8 HIV-infected patients, and 8 controls]. Overall, 411 genes in white matter were DE in HAND with HIVE patients when comparing with controls. Of these, 94 genes were significantly expressed in all statistical methods. These 94 genes participate in significant pathways such as immune system, interferon response, or antigen presentation. Sixty-six of the 94 genes were significantly upregulated with log2 intensities greater than 2-fold. Strong examples of the highly upregulated genes were PSMB8-AS1, APOL6, TRIM69, PSME1, CTSB, HLA-E, GPNMB, UBE2L6, PSME2, NET1, CAPG, B2M, RPL38, GBP1, and PLSCR1. Only BTN3A2 was expressed in HAND with HIVE patients as compared with HAND patients without HIVE. CONCLUSION A number of genes were DE in our meta-analysis that were not identified in the individual analyses. The meta-analytic approach has increased statistical power for identifying DE genes in HAND.
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Bornschein J, Nielitz J, Drozdov I, Selgrad M, Wex T, Jechorek D, Link A, Vieth M, Malfertheiner P. Expression of aurora kinase A correlates with the Wnt-modulator RACGAP1 in gastric cancer. Cancer Med 2016; 5:516-26. [PMID: 26778597 PMCID: PMC4799948 DOI: 10.1002/cam4.610] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 11/19/2015] [Accepted: 11/19/2015] [Indexed: 12/22/2022] Open
Abstract
Canonical Wnt signaling is involved in gastric carcinogenesis. The aim of this study was to identify the link between Wnt signaling and aurora kinase A (AURKA), a target for the treatment of gastrointestinal cancers. Publicly available microarray data were used to identify phenotype‐specific protein–protein interaction (PPI) subnetworks. The in silico analysis revealed a gastric cancer‐specific PPI subnetwork consisting of 2745 proteins and 50,935 interactions. We focused on the link of AURKA to a Wnt‐specific interaction module consisting of 92 proteins. There was a direct association of AURKA with Rac GTPase‐activating protein 1 (RACGAP1), as well as with CTNBB1 (β‐catenin) and CDKN1A as second‐order interactors. Differential expression analysis revealed a significant downregulation of both AURKA and RACGAP1 in gastric cancer compared to noncancer controls. Biopsies from a prospective cohort of 56 patients with gastric cancer (32 intestinal type, 24 diffuse type) and 20 noncancer controls were used for validation of the identified targets. The RT‐PCR data confirmed a strong correlation of AURKA and RACGAP1 gene expression both in the tumor, the tumor‐adjacent and the tumor‐distant mucosa. RACGAP1 in the tumor was also associated with CTNBB1 expression, and inversely associated with CDKN1A gene expression. Immunohistochemistry confirmed expression of the RACGAP1 protein in gastric cancer and the tumor‐adjacent mucosa. RACGAP1 expression was not associated with tumor stage, grading, Lauren type, Helicobacter pylori infection, or age. In conclusion, AURKA is directly associated with the expression of RACGAP1, a modulator of the canonical Wnt signaling pathway.
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Affiliation(s)
- Jan Bornschein
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Leipziger Str. 44, 39120, Magdeburg, Germany
| | - Jessica Nielitz
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Leipziger Str. 44, 39120, Magdeburg, Germany
| | - Ignat Drozdov
- Department of Computational Biology, Bering Limited, 80 Third Cross Road, Twickenham, TW2 5EA, United Kingdom
| | - Michael Selgrad
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Leipziger Str. 44, 39120, Magdeburg, Germany
| | - Thomas Wex
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Leipziger Str. 44, 39120, Magdeburg, Germany.,Department of Molecular Genetics, Medical Laboratory for Clinical Chemistry, Microbiology and Infectious Diseases, Am Neustädter Feld 47, 39124, Magdeburg, Germany
| | - Doerthe Jechorek
- Institute of Pathology, Otto-von-Guericke University, Leipziger Str. 44, 39120, Magdeburg, Germany
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Leipziger Str. 44, 39120, Magdeburg, Germany
| | - Michael Vieth
- Institute of Pathology, Otto-von-Guericke University, Leipziger Str. 44, 39120, Magdeburg, Germany.,Institute of Pathology, Klinikum Bayreuth GmbH, Preuschwitzer Str. 101, 95445, Bayreuth, Germany
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University, Leipziger Str. 44, 39120, Magdeburg, Germany
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Lazic SE. Ranking, selecting, and prioritising genes with desirability functions. PeerJ 2015; 3:e1444. [PMID: 26644980 PMCID: PMC4671156 DOI: 10.7717/peerj.1444] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/05/2015] [Indexed: 11/20/2022] Open
Abstract
In functional genomics experiments, researchers often select genes to follow-up or validate from a long list of differentially expressed genes. Typically, sharp thresholds are used to bin genes into groups such as significant/non-significant or fold change above/below a cut-off value, and ad hoc criteria are also used such as favouring well-known genes. Binning, however, is inefficient and does not take the uncertainty of the measurements into account. Furthermore, p-values, fold-changes, and other outcomes are treated as equally important, and relevant genes may be overlooked with such an approach. Desirability functions are proposed as a way to integrate multiple selection criteria for ranking, selecting, and prioritising genes. These functions map any variable to a continuous 0–1 scale, where one is maximally desirable and zero is unacceptable. Multiple selection criteria are then combined to provide an overall desirability that is used to rank genes. In addition to p-values and fold-changes, further experimental results and information contained in databases can be easily included as criteria. The approach is demonstrated with a breast cancer microarray data set. The functions and an example data set can be found in the desiR package on CRAN (https://cran.r-project.org/web/packages/desiR/) and the development version is available on GitHub (https://github.com/stanlazic/desiR).
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Affiliation(s)
- Stanley E Lazic
- In Silico Lead Discovery, Novartis Institutes for Biomedical Research , Basel , Switzerland
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Kim S, Schliekelman P. Prioritizing hypothesis tests for high throughput data. ACTA ACUST UNITED AC 2015; 32:850-8. [PMID: 26576654 DOI: 10.1093/bioinformatics/btv608] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 10/16/2015] [Indexed: 11/14/2022]
Abstract
MOTIVATION The advent of high throughput data has led to a massive increase in the number of hypothesis tests conducted in many types of biological studies and a concomitant increase in stringency of significance thresholds. Filtering methods, which use independent information to eliminate less promising tests and thus reduce multiple testing, have been widely and successfully applied. However, key questions remain about how to best apply them: When is filtering beneficial and when is it detrimental? How good does the independent information need to be in order for filtering to be effective? How should one choose the filter cutoff that separates tests that pass the filter from those that don't? RESULT We quantify the effect of the quality of the filter information, the filter cutoff and other factors on the effectiveness of the filter and show a number of results: If the filter has a high probability (e.g. 70%) of ranking true positive features highly (e.g. top 10%), then filtering can lead to dramatic increase (e.g. 10-fold) in discovery probability when there is high redundancy in information between hypothesis tests. Filtering is less effective when there is low redundancy between hypothesis tests and its benefit decreases rapidly as the quality of the filter information decreases. Furthermore, the outcome is highly dependent on the choice of filter cutoff. Choosing the cutoff without reference to the data will often lead to a large loss in discovery probability. However, naïve optimization of the cutoff using the data will lead to inflated type I error. We introduce a data-based method for choosing the cutoff that maintains control of the family-wise error rate via a correction factor to the significance threshold. Application of this approach offers as much as a several-fold advantage in discovery probability relative to no filtering, while maintaining type I error control. We also introduce a closely related method of P-value weighting that further improves performance. AVAILABILITY AND IMPLEMENTATION R code for calculating the correction factor is available at http://www.stat.uga.edu/people/faculty/paul-schliekelman CONTACT pdschlie@stat.uga.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sangjin Kim
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Paul Schliekelman
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
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Bijangi-Vishehsaraei K, Blum K, Zhang H, Safa AR, Halum SL. Microarray Analysis Gene Expression Profiles in Laryngeal Muscle After Recurrent Laryngeal Nerve Injury. Ann Otol Rhinol Laryngol 2015; 125:247-56. [PMID: 26530091 DOI: 10.1177/0003489415608866] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVES The pathophysiology of recurrent laryngeal nerve (RLN) transection injury is rare in that it is characteristically followed by a high degree of spontaneous reinnervation, with reinnervation of the laryngeal adductor complex (AC) preceding that of the abducting posterior cricoarytenoid (PCA) muscle. Here, we aim to elucidate the differentially expressed myogenic factors following RLN injury that may be at least partially responsible for the spontaneous reinnervation. METHODS F344 male rats underwent RLN injury (n = 12) or sham surgery (n = 12). One week after RLN injury, larynges were harvested following euthanasia. The mRNA was extracted from PCA and AC muscles bilaterally, and microarray analysis was performed using a full rat genome array. RESULTS Microarray analysis of denervated AC and PCA muscles demonstrated dramatic differences in gene expression profiles, with 205 individual probes that were differentially expressed between the denervated AC and PCA muscles and only 14 genes with similar expression patterns. CONCLUSIONS The differential expression patterns of the AC and PCA suggest different mechanisms of reinnervation. The PCA showed the gene patterns of Wallerian degeneration, while the AC expressed the gene patterns of reinnervation by adjacent axonal sprouting. This finding may reveal important therapeutic targets applicable to RLN and other peripheral nerve injuries.
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Affiliation(s)
| | - Kevin Blum
- Purdue University Weldon School of Biomedical Engineering, West Lafayette, Indiana, USA
| | - Hongji Zhang
- Department of Pharmacology and Toxicology, Indiana University, Indianapolis, Indiana, USA
| | - Ahmad R Safa
- Department of Pharmacology and Toxicology, Indiana University, Indianapolis, Indiana, USA
| | - Stacey L Halum
- Department of Speech, Language, and Hearing Sciences, Purdue University, West Lafayette, Indiana, USA
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Kidd M, Drozdov I, Modlin I. Blood and tissue neuroendocrine tumor gene cluster analysis correlate, define hallmarks and predict disease status. Endocr Relat Cancer 2015; 22:561-75. [PMID: 26037279 DOI: 10.1530/erc-15-0092] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/02/2015] [Indexed: 12/13/2022]
Abstract
A multianalyte algorithmic assay (MAAA) identifies circulating neuroendocrine tumor (NET) transcripts (n=51) with a sensitivity/specificity of 98%/97%. We evaluated whether blood measurements correlated with tumor tissue transcript analysis. The latter were segregated into gene clusters (GC) that defined clinical 'hallmarks' of neoplasia. A MAAA/cluster integrated algorithm (CIA) was developed as a predictive activity index to define tumor behavior and outcome. We evaluated three groups. Group 1: publically available NET transcriptome databases (n=15; GeneProfiler). Group 2: prospectively collected tumors and matched blood samples (n=22; qRT-PCR). Group 3: prospective clinical blood samples, n=159: stable disease (SD): n=111 and progressive disease (PD): n=48. Regulatory network analysis, linear modeling, principal component analysis (PCA), and receiver operating characteristic analyses were used to delineate neoplasia 'hallmarks' and assess GC predictive utility. Our results demonstrated: group 1: NET transcriptomes identified (92%) genes elevated. Group 2: 98% genes elevated by qPCR (fold change >2, P<0.05). Correlation analysis of matched blood/tumor was highly significant (R(2)=0.7, P<0.0001), and 58% of genes defined nine omic clusters (SSTRome, proliferome, signalome, metabolome, secretome, epigenome, plurome, and apoptome). Group 3: six clusters (SSTRome, proliferome, metabolome, secretome, epigenome, and plurome) differentiated SD from PD (area under the curve (AUC)=0.81). Integration with blood-algorithm amplified the AUC to 0.92±0.02 for differentiating PD and SD. The CIA defined a significantly lower SD score (34.1±2.6%) than in PD (84±2.8%, P<0.0001). In conclusion, circulating transcripts measurements reflect NET tissue values. Integration of biologically relevant GC differentiate SD from PD. Combination of GC data with the blood-algorithm predicted disease status in >92%. Blood transcript measurement predicts NET activity.
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Affiliation(s)
- Mark Kidd
- Wren Laboratories35 NE Industrial Road, Branford, Connecticut 06405, USA
| | - Ignat Drozdov
- Wren Laboratories35 NE Industrial Road, Branford, Connecticut 06405, USA
| | - Irvin Modlin
- Wren Laboratories35 NE Industrial Road, Branford, Connecticut 06405, USA
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Tsuchiya M, Giuliani A, Hashimoto M, Erenpreisa J, Yoshikawa K. Emergent Self-Organized Criticality in Gene Expression Dynamics: Temporal Development of Global Phase Transition Revealed in a Cancer Cell Line. PLoS One 2015; 10:e0128565. [PMID: 26067993 PMCID: PMC4465832 DOI: 10.1371/journal.pone.0128565] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 04/28/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The underlying mechanism of dynamic control of the genome-wide expression is a fundamental issue in bioscience. We addressed it in terms of phase transition by a systemic approach based on both density analysis and characteristics of temporal fluctuation for the time-course mRNA expression in differentiating MCF-7 breast cancer cells. METHODOLOGY In a recent work, we suggested criticality as an essential aspect of dynamic control of genome-wide gene expression. Criticality was evident by a unimodal-bimodal transition through flattened unimodal expression profile. The flatness on the transition suggests the existence of a critical transition at which up- and down-regulated expression is balanced. Mean field (averaging) behavior of mRNAs based on the temporal expression changes reveals a sandpile type of transition in the flattened profile. Furthermore, around the transition, a self-similar unimodal-bimodal transition of the whole expression occurs in the density profile of an ensemble of mRNA expression. These singular and scaling behaviors identify the transition as the expression phase transition driven by self-organized criticality (SOC). PRINCIPAL FINDINGS Emergent properties of SOC through a mean field approach are revealed: i) SOC, as a form of genomic phase transition, consolidates distinct critical states of expression, ii) Coupling of coherent stochastic oscillations between critical states on different time-scales gives rise to SOC, and iii) Specific gene clusters (barcode genes) ranging in size from kbp to Mbp reveal similar SOC to genome-wide mRNA expression and ON-OFF synchronization to critical states. This suggests that the cooperative gene regulation of topological genome sub-units is mediated by the coherent phase transitions of megadomain-scaled conformations between compact and swollen chromatin states. CONCLUSION AND SIGNIFICANCE In summary, our study provides not only a systemic method to demonstrate SOC in whole-genome expression, but also introduces novel, physically grounded concepts for a breakthrough in the study of biological regulation.
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Affiliation(s)
- Masa Tsuchiya
- Systems Biology Program, School of Media and Governance, Keio University, Fujisawa, Japan
| | - Alessandro Giuliani
- Environment and Health Department, Istituto Superiore di Sanitá, Rome, Italy
| | - Midori Hashimoto
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
| | | | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
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Ferber K, Archer KJ. Modeling discrete survival time using genomic feature data. Cancer Inform 2015; 14:37-43. [PMID: 25861216 PMCID: PMC4360712 DOI: 10.4137/cin.s17275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/18/2014] [Accepted: 12/25/2014] [Indexed: 01/31/2023] Open
Abstract
Researchers have recently shown that penalized models perform well when applied to high-throughput genomic data. Previous researchers introduced the generalized monotone incremental forward stagewise (GMIFS) method for fitting overparameterized logistic regression models. The GMIFS method was subsequently extended by others for fitting several different logit link ordinal response models to high-throughput genomic data. In this study, we further extended the GMIFS method for ordinal response modeling using a complementary log-log link, which allows one to model discrete survival data. We applied our extension to a publicly available microarray gene expression dataset (GSE53733) with a discrete survival outcome. The dataset included 70 primary glioblastoma samples from patients of the German Glioma Network with long-, intermediate-, and short-term overall survival. We tested the performance of our method by examining the prediction accuracy of the fitted model. The method has been implemented as an addition to the ordinalgmifs package in the R programming environment.
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Affiliation(s)
- Kyle Ferber
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Kellie J Archer
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
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Mayrink VD, Lucas JE. Bayesian factor models for the detection of coherent patterns in gene expression data. BRAZ J PROBAB STAT 2015. [DOI: 10.1214/13-bjps226] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Li MD, Wang J, Niu T, Ma JZ, Seneviratne C, Ait-Daoud N, Saadvandi J, Morris R, Weiss D, Campbell J, Haning W, Mawhinney DJ, Weis D, McCann M, Stock C, Kahn R, Iturriaga E, Yu E, Elkashef A, Johnson BA. Transcriptome profiling and pathway analysis of genes expressed differentially in participants with or without a positive response to topiramate treatment for methamphetamine addiction. BMC Med Genomics 2014; 7:65. [PMID: 25495887 PMCID: PMC4279796 DOI: 10.1186/s12920-014-0065-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/19/2014] [Indexed: 01/25/2023] Open
Abstract
Background Developing efficacious medications to treat methamphetamine dependence is a global challenge in public health. Topiramate (TPM) is undergoing evaluation for this indication. The molecular mechanisms underlying its effects are largely unknown. Examining the effects of TPM on genome-wide gene expression in methamphetamine addicts is a clinically and scientifically important component of understanding its therapeutic profile. Methods In this double-blind, placebo-controlled clinical trial, 140 individuals who met the DSM-IV criteria for methamphetamine dependence were randomized to receive either TPM or placebo, of whom 99 consented to participate in our genome-wide expression study. The RNA samples were collected from whole blood for 50 TPM- and 49 placebo-treated participants at three time points: baseline and the ends of weeks 8 and 12. Genome-wide expression profiles and pathways of the two groups were compared for the responders and non-responders at Weeks 8 and 12. To minimize individual variations, expression of all examined genes at Weeks 8 and 12 were normalized to the values at baseline prior to identification of differentially expressed genes and pathways. Results At the single-gene level, we identified 1054, 502, 204, and 404 genes at nominal P values < 0.01 in the responders vs. non-responders at Weeks 8 and 12 for the TPM and placebo groups, respectively. Among them, expression of 159, 38, 2, and 21 genes was still significantly different after Bonferroni corrections for multiple testing. Many of these genes, such as GRINA, PRKACA, PRKCI, SNAP23, and TRAK2, which are involved in glutamate receptor and GABA receptor signaling, are direct targets for TPM. In contrast, no TPM drug targets were identified in the 38 significant genes for the Week 8 placebo group. Pathway analyses based on nominally significant genes revealed 27 enriched pathways shared by the Weeks 8 and 12 TPM groups. These pathways are involved in relevant physiological functions such as neuronal function/synaptic plasticity, signal transduction, cardiovascular function, and inflammation/immune function. Conclusion Topiramate treatment of methamphetamine addicts significantly modulates the expression of genes involved in multiple biological processes underlying addiction behavior and other physiological functions. Electronic supplementary material The online version of this article (doi:10.1186/s12920-014-0065-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming D Li
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, USA.
| | - Ju Wang
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, USA.
| | - Tianhua Niu
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, USA.
| | - Jennie Z Ma
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, USA.
| | | | - Nassima Ait-Daoud
- Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, USA.
| | | | - Rana Morris
- Information Management Consultants, Reston, USA.
| | - David Weiss
- Department of Veterans Affairs Cooperative Studies Program Coordination Center, Perry Point, USA.
| | - Jan Campbell
- Department of Psychiatry, University of Missouri, Kansas City, USA.
| | | | | | - Denis Weis
- Lutheran Hospital Office of Research, Des Moines, USA.
| | | | - Christopher Stock
- Department of Veterans Affairs, Salt Lake City Health Care System, Salt Lake City, USA.
| | - Roberta Kahn
- Division of Pharmacotherapies and Medical Consequences of Drug Abuse, NIDA, Bethesda, USA.
| | - Erin Iturriaga
- Division of Pharmacotherapies and Medical Consequences of Drug Abuse, NIDA, Bethesda, USA.
| | - Elmer Yu
- Veterans Administration Medical Center, Philadelphia, USA.
| | - Ahmed Elkashef
- Division of Pharmacotherapies and Medical Consequences of Drug Abuse, NIDA, Bethesda, USA.
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DeSalvo MK, Hindle SJ, Rusan ZM, Orng S, Eddison M, Halliwill K, Bainton RJ. The Drosophila surface glia transcriptome: evolutionary conserved blood-brain barrier processes. Front Neurosci 2014; 8:346. [PMID: 25426014 PMCID: PMC4224204 DOI: 10.3389/fnins.2014.00346] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 10/10/2014] [Indexed: 12/29/2022] Open
Abstract
Central nervous system (CNS) function is dependent on the stringent regulation of metabolites, drugs, cells, and pathogens exposed to the CNS space. Cellular blood-brain barrier (BBB) structures are highly specific checkpoints governing entry and exit of all small molecules to and from the brain interstitial space, but the precise mechanisms that regulate the BBB are not well understood. In addition, the BBB has long been a challenging obstacle to the pharmacologic treatment of CNS diseases; thus model systems that can parse the functions of the BBB are highly desirable. In this study, we sought to define the transcriptome of the adult Drosophila melanogaster BBB by isolating the BBB surface glia with fluorescence activated cell sorting (FACS) and profiling their gene expression with microarrays. By comparing the transcriptome of these surface glia to that of all brain glia, brain neurons, and whole brains, we present a catalog of transcripts that are selectively enriched at the Drosophila BBB. We found that the fly surface glia show high expression of many ATP-binding cassette (ABC) and solute carrier (SLC) transporters, cell adhesion molecules, metabolic enzymes, signaling molecules, and components of xenobiotic metabolism pathways. Using gene sequence-based alignments, we compare the Drosophila and Murine BBB transcriptomes and discover many shared chemoprotective and small molecule control pathways, thus affirming the relevance of invertebrate models for studying evolutionary conserved BBB properties. The Drosophila BBB transcriptome is valuable to vertebrate and insect biologists alike as a resource for studying proteins underlying diffusion barrier development and maintenance, glial biology, and regulation of drug transport at tissue barriers.
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Affiliation(s)
- Michael K DeSalvo
- Department of Anesthesia and Perioperative Care, University of California San Francisco San Francisco, CA, USA
| | - Samantha J Hindle
- Department of Anesthesia and Perioperative Care, University of California San Francisco San Francisco, CA, USA
| | - Zeid M Rusan
- Department of Anesthesia and Perioperative Care, University of California San Francisco San Francisco, CA, USA
| | - Souvinh Orng
- Department of Anesthesia and Perioperative Care, University of California San Francisco San Francisco, CA, USA
| | - Mark Eddison
- Janelia Farm Research Campus, The Howard Hughes Medical Institute Ashburn, VA, USA
| | - Kyle Halliwill
- Pharmaceutical Sciences and Pharmacogenomics, University of California San Francisco San Francisco, CA, USA
| | - Roland J Bainton
- Department of Anesthesia and Perioperative Care, University of California San Francisco San Francisco, CA, USA
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McClintick JN, Brooks AI, Deng L, Liang L, Wang JC, Kapoor M, Xuei X, Foroud T, Tischfield JA, Edenberg HJ. Ethanol treatment of lymphoblastoid cell lines from alcoholics and non-alcoholics causes many subtle changes in gene expression. Alcohol 2014; 48:603-10. [PMID: 25129674 PMCID: PMC4730944 DOI: 10.1016/j.alcohol.2014.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
To elucidate the effects of a controlled exposure to ethanol on gene expression, we studied lymphoblastoid cell lines (LCLs) from 21 alcoholics and 21 controls. We cultured each cell line for 24 h with and without 75 mM ethanol and measured gene expression using microarrays. Differences in expression between LCLs from alcoholics and controls included 13 genes previously identified as associated with alcoholism or related traits, including KCNA3, DICER1, ZNF415, CAT, SLC9A9, and PPARGC1B. The paired design allowed us to detect very small changes due to ethanol treatment: ethanol altered the expression of 37% of the probe sets (51% of the unique named genes) expressed in these LCLs, most by modest amounts. Ninety-nine percent of the named genes expressed in the LCLs were also expressed in brain. Key pathways affected by ethanol include cytokine, TNF, and NFκB signaling. Among the genes affected by ethanol were ANK3, EPHB1, SLC1A1, SLC9A9, NRD1, and SH3BP5, which were reported to be associated with alcoholism or related phenotypes in 2 genome-wide association studies. Genes that either differed in expression between alcoholics and controls or were affected by ethanol exposure are candidates for further study.
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Affiliation(s)
- Jeanette N McClintick
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Andrew I Brooks
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Li Deng
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Li Liang
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Jen C Wang
- Department of Psychiatry, B8134, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Manav Kapoor
- Department of Psychiatry, B8134, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA
| | - Xiaoling Xuei
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jay A Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ, USA
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.
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Yadav RK, Tavakkoli M, Xie M, Girke T, Reddy GV. A high-resolution gene expression map of the Arabidopsis shoot meristem stem cell niche. Development 2014; 141:2735-44. [PMID: 24961803 DOI: 10.1242/dev.106104] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The shoot apical meristem (SAM) acts as a reservoir for stem cells. The central zone (CZ) harbors stem cells. The stem cell progenitors differentiate in the adjacent peripheral zone and in the rib meristem located just beneath the CZ. The SAM is further divided into distinct clonal layers: the L1 epidermal, L2 sub-epidermal and L3 layers. Collectively, SAMs are complex structures that consist of cells of different clonal origins that are organized into functional domains. By employing fluorescence-activated cell sorting, we have generated gene expression profiles of ten cell populations that belong to different clonal layers as well as domains along the central and peripheral axis. Our work reveals that cells in distinct clonal layers exhibit greater diversity in gene expression and greater transcriptional complexity than clonally related cell types in the central and peripheral axis. Assessment of molecular functions and biological processes reveals that epidermal cells express genes involved in pathogen defense: the L2 layer cells express genes involved in DNA repair pathways and telomere maintenance, and the L3 layers express transcripts involved in ion balance and salt tolerance besides photosynthesis. Strikingly, the stem cell-enriched transcriptome comprises very few hormone-responsive transcripts. In addition to providing insights into the expression profiles of hundreds of transcripts, the data presented here will act as a resource for reverse genetic analysis and will be useful in deciphering molecular pathways involved in cell type specification and their functions.
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Affiliation(s)
- Ram Kishor Yadav
- Department of Botany and Plant Sciences, Center for Plant Cell Biology (CEPCEB), Institute of Integrative Genome Biology (IIGB), University of California, Riverside, CA 92521, USA Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali 140306, India
| | - Montreh Tavakkoli
- Department of Botany and Plant Sciences, Center for Plant Cell Biology (CEPCEB), Institute of Integrative Genome Biology (IIGB), University of California, Riverside, CA 92521, USA
| | - Mingtang Xie
- Department of Botany and Plant Sciences, Center for Plant Cell Biology (CEPCEB), Institute of Integrative Genome Biology (IIGB), University of California, Riverside, CA 92521, USA
| | - Thomas Girke
- Department of Botany and Plant Sciences, Center for Plant Cell Biology (CEPCEB), Institute of Integrative Genome Biology (IIGB), University of California, Riverside, CA 92521, USA
| | - G Venugopala Reddy
- Department of Botany and Plant Sciences, Center for Plant Cell Biology (CEPCEB), Institute of Integrative Genome Biology (IIGB), University of California, Riverside, CA 92521, USA
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Kidd M, Modlin IM, Drozdov I. Gene network-based analysis identifies two potential subtypes of small intestinal neuroendocrine tumors. BMC Genomics 2014; 15:595. [PMID: 25023465 PMCID: PMC4124138 DOI: 10.1186/1471-2164-15-595] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 07/07/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Tumor transcriptomes contain information of critical value to understanding the different capacities of a cell at both a physiological and pathological level. In terms of clinical relevance, they provide information regarding the cellular "toolbox" e.g., pathways associated with malignancy and metastasis or drug dependency. Exploration of this resource can therefore be leveraged as a translational tool to better manage and assess neoplastic behavior. The availability of public genome-wide expression datasets, provide an opportunity to reassess neuroendocrine tumors at a more fundamental level. We hypothesized that stringent analysis of expression profiles as well as regulatory networks of the neoplastic cell would provide novel information that facilitates further delineation of the genomic basis of small intestinal neuroendocrine tumors. RESULTS We re-analyzed two publically available small intestinal tumor transcriptomes using stringent quality control parameters and network-based approaches and validated expression of core secretory regulatory elements e.g., CPE, PCSK1, secretogranins, including genes involved in depolarization e.g., SCN3A, as well as transcription factors associated with neurodevelopment (NKX2-2, NeuroD1, INSM1) and glucose homeostasis (APLP1). The candidate metastasis-associated transcription factor, ST18, was highly expressed (>14-fold, p < 0.004). Genes previously associated with neoplasia, CEBPA and SDHD, were decreased in expression (-1.5 - -2, p < 0.02). Genomic interrogation indicated that intestinal tumors may consist of two different subtypes, serotonin-producing neoplasms and serotonin/substance P/tachykinin lesions. QPCR validation in an independent dataset (n = 13 neuroendocrine tumors), confirmed up-regulated expression of 87% of genes (13/15). CONCLUSIONS An integrated cellular transcriptomic analysis of small intestinal neuroendocrine tumors identified that they are regulated at a developmental level, have key activation of hypoxic pathways (a known regulator of malignant stem cell phenotypes) as well as activation of genes involved in apoptosis and proliferation. Further refinement of these analyses by RNAseq studies of large-scale databases will enable definition of individual master regulators and facilitate the development of novel tissue and blood-based tools to better understand diagnose and treat tumors.
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Affiliation(s)
- Mark Kidd
- Yale University School of Medicine, New Haven, CT 06510, USA.
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Lossie AC, Muir WM, Lo CL, Timm F, Liu Y, Gray W, Zhou FC. Implications of genomic signatures in the differential vulnerability to fetal alcohol exposure in C57BL/6 and DBA/2 mice. Front Genet 2014; 5:173. [PMID: 24966868 PMCID: PMC4052096 DOI: 10.3389/fgene.2014.00173] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/22/2014] [Indexed: 12/12/2022] Open
Abstract
Maternal alcohol consumption inflicts a multitude of phenotypic consequences that range from undetectable changes to severe dysmorphology. Using tightly controlled murine studies that deliver precise amounts of alcohol at discrete developmental stages, our group and other labs demonstrated in prior studies that the C57BL/6 and DBA/2 inbred mouse strains display differential susceptibility to the teratogenic effects of alcohol. Since the phenotypic diversity extends beyond the amount, dosage and timing of alcohol exposure, it is likely that an individual's genetic background contributes to the phenotypic spectrum. To identify the genomic signatures associated with these observed differences in alcohol-induced dysmorphology, we conducted a microarray-based transcriptome study that also interrogated the genomic signatures between these two lines based on genetic background and alcohol exposure. This approach is called a gene x environment (GxE) analysis; one example of a GxE interaction would be a gene whose expression level increases in C57BL/6, but decreases in DBA/2 embryos, following alcohol exposure. We identified 35 candidate genes exhibiting GxE interactions. To identify cis-acting factors that mediated these interactions, we interrogated the proximal promoters of these 35 candidates and found 241 single nucleotide variants (SNVs) in 16 promoters. Further investigation indicated that 186 SNVs (15 promoters) are predicted to alter transcription factor binding. In addition, 62 SNVs created, removed or altered the placement of a CpG dinucleotide in 13 of the proximal promoters, 53 of which overlapped putative transcription factor binding sites. These 53 SNVs are also our top candidates for future studies aimed at examining the effects of alcohol on epigenetic gene regulation.
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Affiliation(s)
- Amy C Lossie
- Department of Animal Sciences, Purdue University West Lafayette, IN, USA
| | - William M Muir
- Department of Animal Sciences, Purdue University West Lafayette, IN, USA ; Department of Medicine, Indiana University School of Medicine Indianapolis, IN, USA
| | - Chiao-Ling Lo
- Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA
| | - Floyd Timm
- Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA
| | - Yunlong Liu
- Department of Molecular and Medical Genetics, Indiana University School of Medicine Indianapolis, IN, USA
| | - Whitney Gray
- Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA
| | - Feng C Zhou
- Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA ; Stark Neuroscience Research Institute, Indiana University School of Medicine Indianapolis, IN, USA
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Swindell WR, Xing X, Voorhees JJ, Elder JT, Johnston A, Gudjonsson JE. Integrative RNA-seq and microarray data analysis reveals GC content and gene length biases in the psoriasis transcriptome. Physiol Genomics 2014; 46:533-46. [PMID: 24844236 DOI: 10.1152/physiolgenomics.00022.2014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Gene expression profiling of psoriasis has driven research advances and may soon provide the basis for clinical applications. For expression profiling studies, RNA-seq is now a competitive technology, but RNA-seq results may differ from those obtained by microarray. We therefore compared findings obtained by RNA-seq with those from eight microarray studies of psoriasis. RNA-seq and microarray datasets identified similar numbers of differentially expressed genes (DEGs), with certain genes uniquely identified by each technology. Correspondence between platforms and the balance of increased to decreased DEGs was influenced by mRNA abundance, GC content, and gene length. Weakly expressed genes, genes with low GC content, and long genes were all biased toward decreased expression in psoriasis lesions. The strength of these trends differed among array datasets, most likely due to variations in RNA quality. Gene length bias was by far the strongest trend and was evident in all datasets regardless of the expression profiling technology. The effect was due to differences between lesional and uninvolved skin with respect to the genome-wide correlation between gene length and gene expression, which was consistently more negative in psoriasis lesions. These findings demonstrate the complementary nature of RNA-seq and microarray technology and show that integrative analysis of both data types can provide a richer view of the transcriptome than strict reliance on a single method alone. Our results also highlight factors affecting correspondence between technologies, and we have established that gene length is a major determinant of differential expression in psoriasis lesions.
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Affiliation(s)
- William R Swindell
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Xianying Xing
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - John J Voorhees
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - James T Elder
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Andrew Johnston
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Johann E Gudjonsson
- Department of Dermatology, University of Michigan School of Medicine, Ann Arbor, Michigan
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Eraly SA. Striking differences between knockout and wild-type mice in global gene expression variability. PLoS One 2014; 9:e97734. [PMID: 24830645 PMCID: PMC4022672 DOI: 10.1371/journal.pone.0097734] [Citation(s) in RCA: 8] [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: 09/27/2013] [Accepted: 04/23/2014] [Indexed: 12/16/2022] Open
Abstract
Microarray analyses of gene knockouts have traditionally focused on the identification of genes whose mean expression is different in knockout and wild-type mice. However, recent work suggests that changes in the variability of gene expression can have important phenotypic consequences as well. Here, in an unbiased sample of publicly available microarray data on gene expression in various knockouts, highly significant differences from wild-type (either increases or decreases) are noted in the gene expression coefficients of variation (CVs) of virtually every knockout considered. Examination of the distribution of gene-by-gene CV differences indicates that these findings are not attributable to a few outlier genes, but rather to broadly increased or decreased CV in the various knockouts over all the (tens of thousands of) transcripts assayed. These global differences in variability may reflect either authentic biological effects of the knockouts or merely experimental inconsistencies. However, regardless of the underlying explanation, the variability differences are of importance as they will influence both the statistical detection of gene expression changes and, potentially, the knockout phenotype itself.
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Affiliation(s)
- Satish A. Eraly
- Department of Medicine, University of California San Diego, School of Medicine, La Jolla, California, United States of America
- * E-mail:
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