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Transcriptional profiling of the ductus arteriosus: Comparison of rodent microarrays and human RNA sequencing.
Yarboro MT, Durbin MD, Herington JL, Shelton EL, Zhang T, Ebby CG, Stoller JZ, Clyman RI, Reese J
(2018) Semin Perinatol 42: 212-220
MeSH Terms: Animals, Animals, Newborn, Ductus Arteriosus, Embryo, Mammalian, Gene Expression Profiling, Gene Expression Regulation, Developmental, Genetic Association Studies, Humans, Microarray Analysis, Models, Animal, Rodentia, Sequence Analysis, RNA, Species Specificity, Vascular Patency
Show Abstract · Added November 26, 2018
DA closure is crucial for the transition from fetal to neonatal life. This closure is supported by changes to the DA's signaling and structural properties that distinguish it from neighboring vessels. Examining transcriptional differences between these vessels is key to identifying genes or pathways responsible for DA closure. Several microarray studies have explored the DA transcriptome in animal models but varied experimental designs have led to conflicting results. Thorough transcriptomic analysis of the human DA has yet to be performed. A clear picture of the DA transcriptome is key to guiding future research endeavors, both to allow more targeted treatments in the clinical setting, and to understand the basic biology of DA function. In this review, we use a cross-species cross-platform analysis to consider all available published rodent microarray data and novel human RNAseq data in order to provide high priority candidate genes for consideration in future DA studies.
Copyright © 2018 Elsevier Inc. All rights reserved.
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14 MeSH Terms
Comparative Transcriptome Profiles of Human Blood in Response to the Toll-like Receptor 4 Ligands Lipopolysaccharide and Monophosphoryl Lipid A.
Luan L, Patil NK, Guo Y, Hernandez A, Bohannon JK, Fensterheim BA, Wang J, Xu Y, Enkhbaatar P, Stark R, Sherwood ER
(2017) Sci Rep 7: 40050
MeSH Terms: Adjuvants, Immunologic, Healthy Volunteers, Humans, Immunologic Factors, Leukocytes, Lipid A, Lipopolysaccharides, Microarray Analysis, Toll-Like Receptor 4, Transcriptome
Show Abstract · Added April 6, 2017
Monophosphoryl lipid A (MPLA), a less toxic derivative of lipopolysaccharide (LPS), is employed as a vaccine adjuvant and is under investigation as a non-specific immunomodulator. However, the differential response of human leukocytes to MPLA and LPS has not been well characterized. The goal of this study was to compare the differential transcriptomic response of human blood to LPS and MPLA. Venous blood from human volunteers was stimulated with LPS, MPLA or vehicle. Gene expression was determined using microarray analysis. Among 21,103 probes profiled, 136 and 130 genes were differentially regulated by LPS or MPLA, respectively. Seventy four genes were up-regulated and 9 were down-regulated by both ligands. The remaining genes were differentially induced by either agent. Ingenuity Pathway Analysis predicted that LPS and MPLA share similar upstream regulators and have comparable effects on canonical pathways and cellular functions. However, some pro-inflammatory cytokine and inflammasome-associated transcripts were more strongly induced by LPS. In contrast, only the macrophage-regulating chemokine CCL7 was preferentially up-regulated by MPLA. In conclusion, LPS and MPLA induce similar transcriptional profiles. However, LPS more potently induces pro-inflammatory cytokine and inflammasome-linked transcripts. Thus, MPLA is a less potent activator of the pro-inflammatory response but retains effective immunomodulatory activity.
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10 MeSH Terms
Refinement of Triple-Negative Breast Cancer Molecular Subtypes: Implications for Neoadjuvant Chemotherapy Selection.
Lehmann BD, Jovanović B, Chen X, Estrada MV, Johnson KN, Shyr Y, Moses HL, Sanders ME, Pietenpol JA
(2016) PLoS One 11: e0157368
MeSH Terms: Antineoplastic Agents, Antineoplastic Combined Chemotherapy Protocols, Computational Biology, Datasets as Topic, Disease Progression, Female, Gene Expression, Gene Expression Profiling, Humans, Immunohistochemistry, Laser Capture Microdissection, Lymphocytes, Tumor-Infiltrating, Microarray Analysis, Neoadjuvant Therapy, Neoplasm Grading, Neoplasm Proteins, Retrospective Studies, Stromal Cells, Survival Analysis, Triple Negative Breast Neoplasms
Show Abstract · Added April 9, 2017
Triple-negative breast cancer (TNBC) is a heterogeneous disease that can be classified into distinct molecular subtypes by gene expression profiling. Considered a difficult-to-treat cancer, a fraction of TNBC patients benefit significantly from neoadjuvant chemotherapy and have far better overall survival. Outside of BRCA1/2 mutation status, biomarkers do not exist to identify patients most likely to respond to current chemotherapy; and, to date, no FDA-approved targeted therapies are available for TNBC patients. Previously, we developed an approach to identify six molecular subtypes TNBC (TNBCtype), with each subtype displaying unique ontologies and differential response to standard-of-care chemotherapy. Given the complexity of the varying histological landscape of tumor specimens, we used histopathological quantification and laser-capture microdissection to determine that transcripts in the previously described immunomodulatory (IM) and mesenchymal stem-like (MSL) subtypes were contributed from infiltrating lymphocytes and tumor-associated stromal cells, respectively. Therefore, we refined TNBC molecular subtypes from six (TNBCtype) into four (TNBCtype-4) tumor-specific subtypes (BL1, BL2, M and LAR) and demonstrate differences in diagnosis age, grade, local and distant disease progression and histopathology. Using five publicly available, neoadjuvant chemotherapy breast cancer gene expression datasets, we retrospectively evaluated chemotherapy response of over 300 TNBC patients from pretreatment biopsies subtyped using either the intrinsic (PAM50) or TNBCtype approaches. Combined analysis of TNBC patients demonstrated that TNBC subtypes significantly differ in response to similar neoadjuvant chemotherapy with 41% of BL1 patients achieving a pathological complete response compared to 18% for BL2 and 29% for LAR with 95% confidence intervals (CIs; [33, 51], [9, 28], [17, 41], respectively). Collectively, we provide pre-clinical data that could inform clinical trials designed to test the hypothesis that improved outcomes can be achieved for TNBC patients, if selection and combination of existing chemotherapies is directed by knowledge of molecular TNBC subtypes.
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20 MeSH Terms
Alternate Metabolic Programs Define Regional Variation of Relevant Biological Features in Renal Cell Carcinoma Progression.
Brooks SA, Khandani AH, Fielding JR, Lin W, Sills T, Lee Y, Arreola A, Milowsky MI, Wallen EM, Woods ME, Smith AB, Nielsen ME, Parker JS, Lalush DS, Rathmell WK
(2016) Clin Cancer Res 22: 2950-9
MeSH Terms: Biomarkers, Tumor, Carcinoma, Renal Cell, Disease Progression, Gene Expression Regulation, Neoplastic, Humans, Kidney Neoplasms, Magnetic Resonance Imaging, Microarray Analysis, Positron Emission Tomography Computed Tomography
Show Abstract · Added August 8, 2016
PURPOSE - Clear cell renal cell carcinoma (ccRCC) has recently been redefined as a highly heterogeneous disease. In addition to genetic heterogeneity, the tumor displays risk variability for developing metastatic disease, therefore underscoring the urgent need for tissue-based prognostic strategies applicable to the clinical setting. We have recently employed the novel PET/magnetic resonance (MR) image modality to enrich our understanding of how tumor heterogeneity can relate to gene expression and tumor biology to assist in defining individualized treatment plans.
EXPERIMENTAL DESIGN - ccRCC patients underwent PET/MR imaging, and these images subsequently used to identify areas of varied intensity for sampling. Samples from 8 patients were subjected to histologic, immunohistochemical, and microarray analysis.
RESULTS - Tumor subsamples displayed a range of heterogeneity for common features of hypoxia-inducible factor expression and microvessel density, as well as for features closely linked to metabolic processes, such as GLUT1 and FBP1. In addition, gene signatures linked with disease risk (ccA and ccB) also demonstrated variable heterogeneity, with most tumors displaying a dominant panel of features across the sampled regions. Intriguingly, the ccA- and ccB-classified samples corresponded with metabolic features and functional imaging levels. These correlations further linked a variety of metabolic pathways (i.e., the pentose phosphate and mTOR pathways) with the more aggressive, and glucose avid ccB subtype.
CONCLUSIONS - Higher tumor dependency on exogenous glucose accompanies the development of features associated with the poor risk ccB subgroup. Linking these panels of features may provide the opportunity to create functional maps to enable enhanced visualization of the heterogeneous biologic processes of an individual's disease. Clin Cancer Res; 22(12); 2950-9. ©2016 AACR.
©2016 American Association for Cancer Research.
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9 MeSH Terms
Deletion of the BMP receptor BMPR1a impairs mammary tumor formation and metastasis.
Pickup MW, Hover LD, Guo Y, Gorska AE, Chytil A, Novitskiy SV, Moses HL, Owens P
(2015) Oncotarget 6: 22890-904
MeSH Terms: Animals, Bone Morphogenetic Protein Receptors, Type I, Breast Neoplasms, Humans, Mice, Mice, Inbred C57BL, Microarray Analysis, Neoplasm Metastasis, Signal Transduction
Show Abstract · Added February 5, 2016
Bone Morphogenetic Proteins (BMPs) are secreted cytokines/growth factors belonging to the Transforming Growth Factor β (TGFβ) family. BMP ligands have been shown to be overexpressed in human breast cancers. Normal and cancerous breast tissue display active BMP signaling as indicated by phosphorylated Smads 1, 5 and 9. We combined mice expressing the MMTV.PyMT oncogene with mice having conditional knockout (cKO) of BMP receptor type 1a (BMPR1a) using whey acidic protein (WAP)-Cre and found this deletion resulted in delayed tumor onset and significantly extended survival. Immunofluorescence staining revealed that cKO tumors co-expressed Keratin 5 and mesenchymal cell markers such as Vimentin. This indicates that epithelial-to-mesenchymal (EMT)-like transitions occurred in cKO tumors. We performed microarray analysis on these tumors and found changes that support EMT-like changes. We established primary tumor cell lines and found that BMPR1a cKO had slower growth in vitro and in vivo upon implantation. cKO tumor cells had reduced migration in vitro. We analyzed human databases from TCGA and survival data from microarrays to confirm BMPR1a tumor promoting functions, and found that high BMPR1a gene expression correlates with decreased survival regardless of molecular breast cancer subtype. In conclusion, the data indicate that BMP signaling through BMPR1a functions as a tumor promoter.
1 Communities
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9 MeSH Terms
Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer.
Michailidou K, Beesley J, Lindstrom S, Canisius S, Dennis J, Lush MJ, Maranian MJ, Bolla MK, Wang Q, Shah M, Perkins BJ, Czene K, Eriksson M, Darabi H, Brand JS, Bojesen SE, Nordestgaard BG, Flyger H, Nielsen SF, Rahman N, Turnbull C, BOCS, Fletcher O, Peto J, Gibson L, dos-Santos-Silva I, Chang-Claude J, Flesch-Janys D, Rudolph A, Eilber U, Behrens S, Nevanlinna H, Muranen TA, Aittomäki K, Blomqvist C, Khan S, Aaltonen K, Ahsan H, Kibriya MG, Whittemore AS, John EM, Malone KE, Gammon MD, Santella RM, Ursin G, Makalic E, Schmidt DF, Casey G, Hunter DJ, Gapstur SM, Gaudet MM, Diver WR, Haiman CA, Schumacher F, Henderson BE, Le Marchand L, Berg CD, Chanock SJ, Figueroa J, Hoover RN, Lambrechts D, Neven P, Wildiers H, van Limbergen E, Schmidt MK, Broeks A, Verhoef S, Cornelissen S, Couch FJ, Olson JE, Hallberg E, Vachon C, Waisfisz Q, Meijers-Heijboer H, Adank MA, van der Luijt RB, Li J, Liu J, Humphreys K, Kang D, Choi JY, Park SK, Yoo KY, Matsuo K, Ito H, Iwata H, Tajima K, Guénel P, Truong T, Mulot C, Sanchez M, Burwinkel B, Marme F, Surowy H, Sohn C, Wu AH, Tseng CC, Van Den Berg D, Stram DO, González-Neira A, Benitez J, Zamora MP, Perez JI, Shu XO, Lu W, Gao YT, Cai H, Cox A, Cross SS, Reed MW, Andrulis IL, Knight JA, Glendon G, Mulligan AM, Sawyer EJ, Tomlinson I, Kerin MJ, Miller N, kConFab Investigators, AOCS Group, Lindblom A, Margolin S, Teo SH, Yip CH, Taib NA, Tan GH, Hooning MJ, Hollestelle A, Martens JW, Collée JM, Blot W, Signorello LB, Cai Q, Hopper JL, Southey MC, Tsimiklis H, Apicella C, Shen CY, Hsiung CN, Wu PE, Hou MF, Kristensen VN, Nord S, Alnaes GI, NBCS, Giles GG, Milne RL, McLean C, Canzian F, Trichopoulos D, Peeters P, Lund E, Sund M, Khaw KT, Gunter MJ, Palli D, Mortensen LM, Dossus L, Huerta JM, Meindl A, Schmutzler RK, Sutter C, Yang R, Muir K, Lophatananon A, Stewart-Brown S, Siriwanarangsan P, Hartman M, Miao H, Chia KS, Chan CW, Fasching PA, Hein A, Beckmann MW, Haeberle L, Brenner H, Dieffenbach AK, Arndt V, Stegmaier C, Ashworth A, Orr N, Schoemaker MJ, Swerdlow AJ, Brinton L, Garcia-Closas M, Zheng W, Halverson SL, Shrubsole M, Long J, Goldberg MS, Labrèche F, Dumont M, Winqvist R, Pylkäs K, Jukkola-Vuorinen A, Grip M, Brauch H, Hamann U, Brüning T, GENICA Network, Radice P, Peterlongo P, Manoukian S, Bernard L, Bogdanova NV, Dörk T, Mannermaa A, Kataja V, Kosma VM, Hartikainen JM, Devilee P, Tollenaar RA, Seynaeve C, Van Asperen CJ, Jakubowska A, Lubinski J, Jaworska K, Huzarski T, Sangrajrang S, Gaborieau V, Brennan P, McKay J, Slager S, Toland AE, Ambrosone CB, Yannoukakos D, Kabisch M, Torres D, Neuhausen SL, Anton-Culver H, Luccarini C, Baynes C, Ahmed S, Healey CS, Tessier DC, Vincent D, Bacot F, Pita G, Alonso MR, Álvarez N, Herrero D, Simard J, Pharoah PP, Kraft P, Dunning AM, Chenevix-Trench G, Hall P, Easton DF
(2015) Nat Genet 47: 373-80
MeSH Terms: Breast Neoplasms, Case-Control Studies, Cohort Studies, Female, Genetic Loci, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Meta-Analysis as Topic, Microarray Analysis, Polymorphism, Single Nucleotide
Show Abstract · Added September 28, 2015
Genome-wide association studies (GWAS) and large-scale replication studies have identified common variants in 79 loci associated with breast cancer, explaining ∼14% of the familial risk of the disease. To identify new susceptibility loci, we performed a meta-analysis of 11 GWAS, comprising 15,748 breast cancer cases and 18,084 controls together with 46,785 cases and 42,892 controls from 41 studies genotyped on a 211,155-marker custom array (iCOGS). Analyses were restricted to women of European ancestry. We generated genotypes for more than 11 million SNPs by imputation using the 1000 Genomes Project reference panel, and we identified 15 new loci associated with breast cancer at P < 5 × 10(-8). Combining association analysis with ChIP-seq chromatin binding data in mammary cell lines and ChIA-PET chromatin interaction data from ENCODE, we identified likely target genes in two regions: SETBP1 at 18q12.3 and RNF115 and PDZK1 at 1q21.1. One association appears to be driven by an amino acid substitution encoded in EXO1.
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11 MeSH Terms
miR-216a regulates snx5, a novel notch signaling pathway component, during zebrafish retinal development.
Olena AF, Rao MB, Thatcher EJ, Wu SY, Patton JG
(2015) Dev Biol 400: 72-81
MeSH Terms: Analysis of Variance, Animals, Cloning, Molecular, DNA Primers, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Knockdown Techniques, Image Processing, Computer-Assisted, Immunoblotting, In Situ Hybridization, Intracellular Signaling Peptides and Proteins, Membrane Proteins, MicroRNAs, Microarray Analysis, Models, Biological, Receptors, Notch, Retina, Signal Transduction, Sorting Nexins, Ubiquitin-Protein Ligases, Zebrafish, Zebrafish Proteins
Show Abstract · Added February 4, 2016
Precise regulation of Notch signaling is essential for normal vertebrate development. Mind bomb (Mib) is a ubiquitin ligase that is required for activation of Notch by Notch׳s ligand, Delta. Sorting Nexin 5 (SNX5) co-localizes with Mib and Delta complexes and has been shown to directly bind to Mib. We show that microRNA-216a (miR-216a) is expressed in the retina during early development and regulates snx5 to precisely regulate Notch signaling. miR-216a and snx5 have complementary expression patterns. Knocking down miR-216a and/or overexpression of snx5 resulted in increased Notch activation. Conversely, knocking down snx5 and/or miR-216a overexpression caused a decrease in Notch activation. We propose a model in which SNX5, precisely controlled by miR-216a, is a vital partner of Mib in promoting endocytosis of Delta and subsequent activation of Notch signaling.
Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
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22 MeSH Terms
Peripheral blood signature of vasodilator-responsive pulmonary arterial hypertension.
Hemnes AR, Trammell AW, Archer SL, Rich S, Yu C, Nian H, Penner N, Funke M, Wheeler L, Robbins IM, Austin ED, Newman JH, West J
(2015) Circulation 131: 401-9; discussion 409
MeSH Terms: Adolescent, Adult, Cells, Cultured, Cohort Studies, Female, Humans, Hypertension, Pulmonary, Lymphocytes, Male, Microarray Analysis, Middle Aged, Vasodilation, Young Adult
Show Abstract · Added January 20, 2015
BACKGROUND - Heterogeneity in response to treatment of pulmonary arterial hypertension (PAH) is a major challenge to improving outcome in this disease. Although vasodilator-responsive PAH (VR-PAH) accounts for a minority of cases, VR-PAH has a pronounced response to calcium channel blockers and better survival than vasodilator-nonresponsive PAH (VN-PAH). We hypothesized that VR-PAH has a different molecular cause from VN-PAH that can be detected in the peripheral blood.
METHODS AND RESULTS - Microarrays of cultured lymphocytes from VR-PAH and VN-PAH patients followed at Vanderbilt University were performed with quantitative polymerase chain reaction performed on peripheral blood for the 25 most different genes. We developed a decision tree to identify VR-PAH patients on the basis of the results with validation in a second VR-PAH cohort from the University of Chicago. We found broad differences in gene expression patterns on microarray analysis including cell-cell adhesion factors and cytoskeletal and rho-GTPase genes. Thirteen of 25 genes tested in whole blood were significantly different: EPDR1, DSG2, SCD5, P2RY5, MGAT5, RHOQ, UCHL1, ZNF652, RALGPS2, TPD52, MKNL1, RAPGEF2, and PIAS1. Seven decision trees were built with the use of expression levels of 2 genes as the primary genes: DSG2, a desmosomal cadherin involved in Wnt/β-catenin signaling, and RHOQ, which encodes a cytoskeletal protein involved in insulin-mediated signaling. These trees correctly identified 5 of 5 VR-PAH patients in the validation cohort.
CONCLUSIONS - VR-PAH and VN-PAH can be differentiated with the use of RNA expression patterns in peripheral blood. These differences may reflect different molecular causes of the 2 PAH phenotypes. This biomarker methodology may identify PAH patients who have a favorable treatment response.
© 2014 American Heart Association, Inc.
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13 MeSH Terms
Short-lag spatial coherence imaging on matrix arrays, part II: Phantom and in vivo experiments.
Jakovljevic M, Byram BC, Hyun D, Dahl JJ, Trahey GE
(2014) IEEE Trans Ultrason Ferroelectr Freq Control 61: 1113-22
MeSH Terms: Adult, Algorithms, Computer Simulation, Equipment Design, Equipment Failure Analysis, Female, Hepatic Artery, Humans, Image Interpretation, Computer-Assisted, Male, Microarray Analysis, Middle Aged, Models, Theoretical, Phantoms, Imaging, Reproducibility of Results, Sensitivity and Specificity, Tomography, Optical Coherence, Ultrasonography
Show Abstract · Added February 19, 2015
In Part I of the paper, we demonstrated through simulation the potential of volumetric short-lag spatial coherence (SLSC) imaging to improve visualization of hypoechoic targets in three dimensions. Here, we demonstrate the application of volumetric SLSC imaging in phantom and in vivo experiments using a clinical 3-D ultrasound scanner and matrix array. Using a custom single-channel acquisition tool, we collected partially beamformed channel data from the fully sampled matrix array at high speeds and created matched Bmode and SLSC volumes of a vessel phantom and in vivo liver vasculature. 2-D and 3-D images rendered from the SLSC volumes display reduced clutter and improved visibility of the vessels when compared with their B-mode counterparts. We use concurrently acquired color Doppler volumes to confirm the presence of the vessels of interest and to define the regions inside the vessels used in contrast and contrast-to-noise ratio (CNR) calculations. SLSC volumes show higher CNR values than their matched B-mode volumes, while the contrast values appear to be similar between the two imaging methods.
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18 MeSH Terms
The effects of frozen tissue storage conditions on the integrity of RNA and protein.
Auer H, Mobley JA, Ayers LW, Bowen J, Chuaqui RF, Johnson LA, Livolsi VA, Lubensky IA, McGarvey D, Monovich LC, Moskaluk CA, Rumpel CA, Sexton KC, Washington MK, Wiles KR, Grizzle WE, Ramirez NC
(2014) Biotech Histochem 89: 518-28
MeSH Terms: Cold Temperature, Freezing, Gene Expression Profiling, Humans, Microarray Analysis, Neoplasms, Proteins, Proteomics, RNA, RNA, Messenger, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Tissue Preservation
Show Abstract · Added October 1, 2014
Unfixed tissue specimens most frequently are stored for long term research uses at either -80° C or in vapor phase liquid nitrogen (VPLN). There is little information concerning the effects such long term storage on tissue RNA or protein available for extraction. Aliquots of 49 specimens were stored for 5-12 years at -80° C or in VPLN. Twelve additional paired specimens were stored for 1 year under identical conditions. RNA was isolated from all tissues and assessed for RNA yield, total RNA integrity and mRNA integrity. Protein stability was analyzed by surface-enhanced or matrix-assisted laser desorption ionization time of flight mass spectrometry (SELDI-TOF-MS, MALDI-TOF-MS) and nano-liquid chromatography electrospray ionization tandem mass spectrometry (nLC-ESI-MS/MS). RNA yield and total RNA integrity showed significantly better results for -80° C storage compared to VPLN storage; the transcripts that were preferentially degraded during VPLN storage were these involved in antigen presentation and processing. No consistent differences were found in the SELDI-TOF-MS, MALDI-TOF-MS or nLC-ESI-MS/MS analyses of specimens stored for more than 8 years at -80° C compared to those stored in VPLN. Long term storage of human research tissues at -80° C provides at least the same quality of RNA and protein as storage in VPLN.
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12 MeSH Terms