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Stepaniants S, Wang IM, Boie Y, Mortimer J, Kennedy B, Elliott M, Hayashi S, Luo H, Wong J, Loy L, Coulter S, Roberts CJ, Hogg JC, Sin DD, O'Neill G, Crackower M, Morris M, Paré PD, Obeidat M. Genes related to emphysema are enriched for ubiquitination pathways. BMC Pulm Med 2014; 14:187. [PMID: 25432663 PMCID: PMC4280711 DOI: 10.1186/1471-2466-14-187] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 11/19/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Increased small airway resistance and decreased lung elasticity contribute to the airflow limitation in chronic obstructive pulmonary disease (COPD). The lesion that corresponds to loss of lung elasticity is emphysema; the small airway obstruction is due to inflammatory narrowing and obliteration. Despite their convergence in altered physiology, different mechanisms contribute to these processes. The relationships between gene expression and these specific phenotypes may be more revealing than comparison with lung function. METHODS We measured the ratio of alveolar surface area to lung volume (SA/V) in lung tissue from 43 smokers. Two samples from 21 subjects, in which SA/V differed by >49 cm2/mL were profiled to select genes whose expression correlated with SA/V. Significant genes were tested for replication in the 22 remaining subjects. RESULTS The level of expression of 181 transcripts was related to SA/V ( p < 0.05). When these genes were tested in the 22 remaining subjects as a replication, thirty of the 181 genes remained significantly associated with SA/V (P < 0.05) and the direction of association was the same in 164/181. Pathway and network analysis revealed enrichment of genes involved in protein ubiquitination, and western blotting showed altered expression of genes involved in protein ubiquitination in obstructed individuals. CONCLUSION This study implicates modified protein ubiquitination and degradation as a potentially important pathway in the pathogenesis of emphysema.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Peter D Paré
- University of British Columbia Centre for Heart and Lung Innovation, St Paul's Hospital, 1081 Burrard St, Vancouver V6Z 1Y6, BC, Canada.
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Dow ER, Banerjee P, Penny MA, Nantz E, Stepaniants S, Ho A, Komocsar WJ, Berclaz PY, Hoffman RW. SAT0005 Human C-Type Lectin Domain Family 4, Member C Gene Expression Level Helps Predict Future Clinical Response to Tabalumab Blockade of Baff in Rheumatoid Arthritis. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2013-eular.1731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Kadam SK, Patel BKR, Jones E, Nguyen TS, Verma LK, Landschulz KT, Stepaniants S, Li B, Brandt JT, Brail LH. Biomarkers of the Hedgehog/Smoothened pathway in healthy volunteers. Am J Transl Res 2012; 4:229-239. [PMID: 22611475 PMCID: PMC3353531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Accepted: 04/15/2012] [Indexed: 06/01/2023]
Abstract
The Hedgehog (Hh) pathway is involved in oncogenic transformation and tumor maintenance. The primary objective of this study was to select surrogate tissue to measure messenger ribonucleic acid (mRNA) levels of Hh pathway genes for measurement of pharmacodynamic effect. Expression of Hh pathway specific genes was measured by quantitative real time polymerase chain reaction (qRT-PCR) and global gene expression using Affymetrix U133 microarrays. Correlations were made between the expression of specific genes determined by qRT-PCR and normalized microarray data. Gene ontology analysis using microarray data for a broader set of Hh pathway genes was performed to identify additional Hh pathway-related markers in the surrogate tissue. RNA extracted from blood, hair follicle, and skin obtained from healthy subjects was analyzed by qRT-PCR for 31 genes, whereas 8 samples were analyzed for a 7-gene subset. Twelve sample sets, each with ≤500 ng total RNA derived from hair, skin, and blood, were analyzed using Affymetrix U133 microarrays. Transcripts for several Hh pathway genes were undetectable in blood using qRT-PCR. Skin was the most desirable matrix, followed by hair follicle. Whether processed by robust multiarray average or microarray suite 5 (MAS5), expression patterns of individual samples showed co-clustered signals; both normalization methods were equally effective for unsupervised analysis. The MAS5- normalized probe sets appeared better suited for supervised analysis. This work provides the basis for selection of a surrogate tissue and an expression analysis-based approach to evaluate pathway-related genes as markers of pharmacodynamic effect with novel inhibitors of the Hh pathway.
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Affiliation(s)
- Sunil K Kadam
- Translational Medicine, Eli Lilly and CompanyIndianapolis, IN 46285, USA
| | - Bharvin K R Patel
- Oncology Discovery, Eli Lilly and CompanyIndianapolis, IN 46285, USA
| | - Emma Jones
- European Early Phase Statistics, Eli Lilly and CompanyIndianapolis, IN 46285, USA
| | - Tuan S Nguyen
- Oncology-Statistics, Eli Lilly and CompanyIndianapolis, IN 46285, USA
| | - Lalit K Verma
- Translational Medicine, Eli Lilly and CompanyIndianapolis, IN 46285, USA
| | | | | | - Bin Li
- Covance Genomic LaboratorySeattle, WA 98109, USA
| | - John T Brandt
- Translational Medicine, Eli Lilly and CompanyIndianapolis, IN 46285, USA
| | - Leslie H Brail
- Oncology Business Unit, Eli Lilly and CompanyIndianapolis, IN 46285
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Puig O, Yuan J, Stepaniants S, Zieba R, Zycband E, Morris M, Coulter S, Yu X, Menke J, Woods J, Chen F, Ramey DR, He X, O'Neill EA, Hailman E, Johns DG, Hubbard BK, Yee Lum P, Wright SD, Desouza MM, Plump A, Reiser V. A gene expression signature that classifies human atherosclerotic plaque by relative inflammation status. ACTA ACUST UNITED AC 2011; 4:595-604. [PMID: 22010137 DOI: 10.1161/circgenetics.111.960773] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND Atherosclerosis is a complex disease requiring improvements in diagnostic techniques and therapeutic treatments. Both improvements will be facilitated by greater exploration of the biology of atherosclerotic plaque. To this end, we carried out large-scale gene expression analysis of human atherosclerotic lesions. METHODS AND RESULTS Whole genome expression analysis of 101 plaques from patients with peripheral artery disease identified a robust gene signature (1514 genes) that is dominated by processes related to Toll-like receptor signaling, T-cell activation, cholesterol efflux, oxidative stress response, inflammatory cytokine production, vasoconstriction, and lysosomal activity. Further analysis of gene expression in microdissected carotid plaque samples revealed that this signature is differentially expressed in macrophage-rich and smooth muscle cell-containing regions. A quantitative PCR gene expression panel and inflammatory composite score were developed on the basis of the atherosclerotic plaque gene signature. When applied to serial sections of carotid plaque, the inflammatory composite score was observed to correlate with histological and morphological features related to plaque vulnerability. CONCLUSIONS The robust mRNA expression signature identified in the present report is associated with pathological features of vulnerable atherosclerotic plaque and may be useful as a source of biomarkers and targets of novel antiatherosclerotic therapies.
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Affiliation(s)
- Oscar Puig
- Department of Molecular Profiling,, Merck Research Laboratories, Rahway, NJ 07033, USA.
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He JQ, Sandford AJ, Wang IM, Stepaniants S, Knight DA, Kicic A, Stick SM, Paré PD. Selection of housekeeping genes for real-time PCR in atopic human bronchial epithelial cells. Eur Respir J 2008; 32:755-62. [PMID: 18417509 DOI: 10.1183/09031936.00129107] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The stability of housekeeping genes (HKGs) is critical when performing real-time quantitative PCR. To date, the stability of common HKGs has not been systematically compared in human airway epithelial cells (AEC) in normal and atopic subjects. Expression levels of 12 HKGs were measured in AECs from a cohort of 30 healthy atopic nonasthmatic or atopic asthmatic children. Gene expression stability was determined using three different Visual Basic for Applications applets (geNorm, NormFinder and BestKeeper). All 12 HKGs were expressed in AECs. However, the hypoxanthine ribosyltransferase and TATA-binding protein genes were excluded from further analysis due to low expression levels. The cyclophilin A gene was ranked the most stable by all three methods. The expression levels of the beta-actin and glyceraldehyde-3-phosphate dehydrogenase genes were significantly different between the three groups of patients, with atopic asthmatics showing the highest expression levels for both genes. The results suggest that the cyclophilin A gene is the most suitable housekeeping gene analysed for expression studies utilising uncultured bronchial airway epithelial cells from healthy and asthmatic children, and highlight the importance of validating housekeeping genes for each experimental model.
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Affiliation(s)
- J-Q He
- UBC James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, 1081 Burrard Street, Vancouver, BC, V6Z 1Y6, Canada.
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Wang IM, Stepaniants S, Boie Y, Mortimer JR, Kennedy B, Elliott M, Hayashi S, Loy L, Coulter S, Cervino S, Harris J, Thornton M, Raubertas R, Roberts C, Hogg JC, Crackower M, O'Neill G, Paré PD. Gene expression profiling in patients with chronic obstructive pulmonary disease and lung cancer. Am J Respir Crit Care Med 2007; 177:402-11. [PMID: 17975202 DOI: 10.1164/rccm.200703-390oc] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RATIONALE Chronic obstructive lung disease (COPD) is a common and disabling lung disease for which there are few therapeutic options. OBJECTIVES We reasoned that gene expression profiling of COPD lungs could reveal previously unidentified disease pathways. METHODS Forty-eight human lung samples were obtained from tissue resected from five nonsmokers, 21 GOLD (Global Initiative for Chronic Obstructive Lung Disease) stage 0, 9 GOLD stage 1, 10 GOLD stage 2, and 3 GOLD stage 3 patients. mRNA from the specimens was profiled using Agilent's Functional ID v2.0 array (Agilent, Santa Clara, CA) containing 23,720 sequences. MEASUREMENTS AND MAIN RESULTS The gene expression pattern was influenced by the percentage of the sample made up of parenchyma. Gene expression was related to forced expiratory flow between 25 and 75% of forced expiratory volume (FEF(25-75%) % predicted) revealing a signature gene set of 203 transcripts. Genes involved in extracellular matrix synthesis/degradation and apoptosis were among the up-regulated genes, whereas genes that participate in antiinflammatory responses were down-regulated. Immunohistochemistry confirmed expression of urokinase plasminogen activator (PLAU), urokinase plasminogen activator receptor (PLAUR), and thrombospondin (THBS1) by alveolar macrophages and airway epithelial cells. Genes in this pathway have been shown to be involved in the activation of transforming growth factor (TGF)-beta1 and matrix metalloproteinases and are subject to inhibition by SERPINE2. Interestingly, both TGF-beta1 and SERPINE2 have been identified as candidate genes in COPD genetic linkage and association studies. CONCLUSIONS The results provide evidence that genes involved in tissue remodeling and repair are differentially regulated in the lungs of obstructed smokers and suggest that they are potential therapeutic targets. Data deposited in GEO at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE8500.
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Affiliation(s)
- I-Ming Wang
- McDonald Research Wing, Room 166, St. Paul's Hospital, 1081 Burrard Street, Vancouver, BC, Canada
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Radich JP, Mao M, Stepaniants S, Biery M, Castle J, Ward T, Schimmack G, Kobayashi S, Carleton M, Lampe J, Linsley PS. Individual-specific variation of gene expression in peripheral blood leukocytes. Genomics 2004; 83:980-8. [PMID: 15177552 DOI: 10.1016/j.ygeno.2003.12.013] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2003] [Revised: 12/23/2003] [Accepted: 12/23/2003] [Indexed: 11/20/2022]
Abstract
DNA microarray technology is used to determine gene expression profiles of various cell types, especially abnormal cells, such as cancer. By contrast, relatively little attention has been given to expression profiling of normal tissues. Here we describe studies of gene expression in peripheral blood leukocytes (PBL) from normal individuals sampled multiple times over periods ranging from several weeks up to 6 months. We demonstrate stable patterns of gene expression that differ between individuals. Among the genes whose expression varies by individual is a group of genes responsive to interferon stimulation. Certain individuals ( approximately 10-20% of those tested) showed higher baseline levels and lower inducibility of these genes in response to in vitro interferon stimulation. These studies demonstrate the feasibility of using DNA microarrays to measure the variations in gene expression of PBL from different individuals in response to environmental and genetic factors.
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Affiliation(s)
- Jerald P Radich
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, D4-100, Seattle, WA 98109, USA.
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Dai H, Meyer M, Stepaniants S, Ziman M, Stoughton R. Use of hybridization kinetics for differentiating specific from non-specific binding to oligonucleotide microarrays. Nucleic Acids Res 2002; 30:e86. [PMID: 12177314 PMCID: PMC134259 DOI: 10.1093/nar/gnf085] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hybridization kinetics were found to be significantly different for specific and non-specific binding of labeled cRNA to surface-bound oligonucleotides on microarrays. We show direct evidence that in a complex sample specific binding takes longer to reach hybridization equilibrium than the non- specific binding. We find that this property can be used to estimate and to correct for the hybridization contributed by non-specific binding. Useful applications are illustrated including the selection of superior oligonucleotides, and the reduction of false positives in exon identification.
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Affiliation(s)
- Hongyue Dai
- Rosetta Inpharmatics, 12040 115th Avenue NE, Kirkland, WA 98034, USA
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Izrailev S, Stepaniants S, Isralewitz B, Kosztin D, Lu H, Molnar F, Wriggers W, Schulten K. Steered Molecular Dynamics. Computational Molecular Dynamics: Challenges, Methods, Ideas 1999. [DOI: 10.1007/978-3-642-58360-5_2] [Citation(s) in RCA: 169] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Abstract
One-dimensional stochastic models demonstrate that molecular dynamics simulations of a few nanoseconds can be used to reconstruct the essential features of the binding potential of macromolecules. This can be accomplished by inducing the unbinding with the help of external forces applied to the molecules, and discounting the irreversible work performed on the system by these forces. The fluctuation-dissipation theorem sets a fundamental limit on the precision with which the binding potential can be reconstructed by this method. The uncertainty in the resulting potential is linearly proportional to the irreversible component of work performed on the system during the simulation. These results provide an a priori estimate of the energy barriers observable in molecular dynamics simulations.
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Affiliation(s)
- M Balsera
- Beckman Institute and Department of Physics, University of Illinois, Urbana 61801, USA
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Abstract
We report molecular dynamics simulations that induce, over periods of 40-500 ps, the unbinding of biotin from avidin by means of external harmonic forces with force constants close to those of AFM cantilevers. The applied forces are sufficiently large to reduce the overall binding energy enough to yield unbinding within the measurement time. Our study complements earlier work on biotin-streptavidin that employed a much larger harmonic force constant. The simulations reveal a variety of unbinding pathways, the role of key residues contributing to adhesion as well as the spatial range over which avidin binds biotin. In contrast to the previous studies, the calculated rupture forces exceed by far those observed. We demonstrate, in the framework of models expressed in terms of one-dimensional Langevin equations with a schematic binding potential, the associated Smoluchowski equations, and the theory of first passage times, that picosecond to nanosecond simulation of ligand unbinding requires such strong forces that the resulting protein-ligand motion proceeds far from the thermally activated regime of millisecond AFM experiments, and that simulated unbinding cannot be readily extrapolated to the experimentally observed rupture.
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Affiliation(s)
- S Izrailev
- Beckman Institute, University of Illinois, Urbana 61801, USA
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Meyerovich AE, Stepaniants S, Lalo F. Statistical quasiparticles in transverse dynamics of gases. Phys Rev B Condens Matter 1995; 52:6808-6821. [PMID: 9981910 DOI: 10.1103/physrevb.52.6808] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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Meyerovich AE, Stepaniants S. Boundary effects and spin waves in spin-polarized quantum gases. Phys Rev B Condens Matter 1994; 49:3400-3408. [PMID: 10011202 DOI: 10.1103/physrevb.49.3400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
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