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Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation.
Gamazon ER, Segrè AV, van de Bunt M, Wen X, Xi HS, Hormozdiari F, Ongen H, Konkashbaev A, Derks EM, Aguet F, Quan J, GTEx Consortium, Nicolae DL, Eskin E, Kellis M, Getz G, McCarthy MI, Dermitzakis ET, Cox NJ, Ardlie KG
(2018) Nat Genet 50: 956-967
MeSH Terms: Disease, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Genome-Wide Association Study, Genotype, Humans, Phenotype, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Quantitative Trait, Heritable
Show Abstract · Added July 1, 2018
We apply integrative approaches to expression quantitative loci (eQTLs) from 44 tissues from the Genotype-Tissue Expression project and genome-wide association study data. About 60% of known trait-associated loci are in linkage disequilibrium with a cis-eQTL, over half of which were not found in previous large-scale whole blood studies. Applying polygenic analyses to metabolic, cardiovascular, anthropometric, autoimmune, and neurodegenerative traits, we find that eQTLs are significantly enriched for trait associations in relevant pathogenic tissues and explain a substantial proportion of the heritability (40-80%). For most traits, tissue-shared eQTLs underlie a greater proportion of trait associations, although tissue-specific eQTLs have a greater contribution to some traits, such as blood pressure. By integrating information from biological pathways with eQTL target genes and applying a gene-based approach, we validate previously implicated causal genes and pathways, and propose new variant and gene associations for several complex traits, which we replicate in the UK BioBank and BioVU.
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11 MeSH Terms
Quantitative in vivo whole genome motility screen reveals novel therapeutic targets to block cancer metastasis.
Stoletov K, Willetts L, Paproski RJ, Bond DJ, Raha S, Jovel J, Adam B, Robertson AE, Wong F, Woolner E, Sosnowski DL, Bismar TA, Wong GK, Zijlstra A, Lewis JD
(2018) Nat Commun 9: 2343
MeSH Terms: Animals, Cell Line, Tumor, Cell Movement, Chick Embryo, Collagen, Female, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Humans, Male, Mice, Mice, Nude, Mice, SCID, Neoplasm Invasiveness, Neoplasm Metastasis, Neoplasm Transplantation, Phenotype, Prostatic Neoplasms, RNA Interference, RNA, Small Interfering
Show Abstract · Added April 10, 2019
Metastasis is the most lethal aspect of cancer, yet current therapeutic strategies do not target its key rate-limiting steps. We have previously shown that the entry of cancer cells into the blood stream, or intravasation, is highly dependent upon in vivo cancer cell motility, making it an attractive therapeutic target. To systemically identify genes required for tumor cell motility in an in vivo tumor microenvironment, we established a novel quantitative in vivo screening platform based on intravital imaging of human cancer metastasis in ex ovo avian embryos. Utilizing this platform to screen a genome-wide shRNA library, we identified a panel of novel genes whose function is required for productive cancer cell motility in vivo, and whose expression is closely associated with metastatic risk in human cancers. The RNAi-mediated inhibition of these gene targets resulted in a nearly total (>99.5%) block of spontaneous cancer metastasis in vivo.
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MeSH Terms
Hypertension and increased endothelial mechanical stretch promote monocyte differentiation and activation: roles of STAT3, interleukin 6 and hydrogen peroxide.
Loperena R, Van Beusecum JP, Itani HA, Engel N, Laroumanie F, Xiao L, Elijovich F, Laffer CL, Gnecco JS, Noonan J, Maffia P, Jasiewicz-Honkisz B, Czesnikiewicz-Guzik M, Mikolajczyk T, Sliwa T, Dikalov S, Weyand CM, Guzik TJ, Harrison DG
(2018) Cardiovasc Res 114: 1547-1563
MeSH Terms: Aged, Angiotensin II, Animals, Blood Pressure, Case-Control Studies, Cell Communication, Cell Differentiation, Cells, Cultured, Coculture Techniques, Disease Models, Animal, Endothelial Cells, Female, Humans, Hydrogen Peroxide, Hypertension, Interleukin-6, Male, Mechanotransduction, Cellular, Mice, Inbred C57BL, Middle Aged, Monocytes, Nitric Oxide, Phenotype, STAT3 Transcription Factor, Stress, Mechanical
Show Abstract · Added March 26, 2019
Aims - Monocytes play an important role in hypertension. Circulating monocytes in humans exist as classical, intermediate, and non-classical forms. Monocyte differentiation can be influenced by the endothelium, which in turn is activated in hypertension by mechanical stretch. We sought to examine the role of increased endothelial stretch and hypertension on monocyte phenotype and function.
Methods and results - Human monocytes were cultured with confluent human aortic endothelial cells undergoing either 5% or 10% cyclical stretch. We also characterized circulating monocytes in normotensive and hypertensive humans. In addition, we quantified accumulation of activated monocytes and monocyte-derived cells in aortas and kidneys of mice with Angiotensin II-induced hypertension. Increased endothelial stretch enhanced monocyte conversion to CD14++CD16+ intermediate monocytes and monocytes bearing the CD209 marker and markedly stimulated monocyte mRNA expression of interleukin (IL)-6, IL-1β, IL-23, chemokine (C-C motif) ligand 4, and tumour necrosis factor α. STAT3 in monocytes was activated by increased endothelial stretch. Inhibition of STAT3, neutralization of IL-6 and scavenging of hydrogen peroxide prevented formation of intermediate monocytes in response to increased endothelial stretch. We also found evidence that nitric oxide (NO) inhibits formation of intermediate monocytes and STAT3 activation. In vivo studies demonstrated that humans with hypertension have increased intermediate and non-classical monocytes and that intermediate monocytes demonstrate evidence of STAT3 activation. Mice with experimental hypertension exhibit increased aortic and renal infiltration of monocytes, dendritic cells, and macrophages with activated STAT3.
Conclusions - These findings provide insight into how monocytes are activated by the vascular endothelium during hypertension. This is likely in part due to a loss of NO signalling and increased release of IL-6 and hydrogen peroxide by the dysfunctional endothelium and a parallel increase in STAT activation in adjacent monocytes. Interventions to enhance bioavailable NO, reduce IL-6 or hydrogen peroxide production or to inhibit STAT3 may have anti-inflammatory roles in hypertension and related conditions.
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25 MeSH Terms
Deletion of Macrophage Low-Density Lipoprotein Receptor-Related Protein 1 (LRP1) Accelerates Atherosclerosis Regression and Increases C-C Chemokine Receptor Type 7 (CCR7) Expression in Plaque Macrophages.
Mueller PA, Zhu L, Tavori H, Huynh K, Giunzioni I, Stafford JM, Linton MF, Fazio S
(2018) Circulation 138: 1850-1863
MeSH Terms: Animals, Aorta, Aortic Diseases, Apoptosis, Atherosclerosis, Cells, Cultured, Cholesterol, Disease Models, Animal, Female, Gene Deletion, Genetic Predisposition to Disease, Macrophages, Mice, Knockout, ApoE, Necrosis, Phenotype, Plaque, Atherosclerotic, Receptors, CCR7, Receptors, LDL, Signal Transduction, Tumor Suppressor Proteins, Up-Regulation
Show Abstract · Added July 20, 2018
BACKGROUND - We previously showed that mice lacking MΦLRP1 (low-density lipoprotein receptor-related protein 1 in macrophages) undergo accelerated atherosclerotic plaque formation due to changes in macrophages including increased apoptosis, decreased efferocytosis, and exaggerated transition to the inflammatory M1 phenotype. Here we sought to explore the role of macrophage low-density lipoprotein receptor-related protein 1 during regression of atherosclerosis since regressing plaques are characterized by transitioning of macrophages to M2 status as inflammation resolves.
METHODS - Apolipoprotein E mice on a high-fat diet for 12 weeks were reconstituted with bone marrow from apolipoprotein E-producing wild-type or MΦLRP1 mice, and then placed on a chow diet for 10 weeks (n=9 to 11 mice/group). A cohort of apolipoprotein E mice reconstituted with apolipoprotein E bone marrow served as baseline controls (n=9).
RESULTS - Plaques of both wild-type and MΦLRP1 bone marrow recipients regressed compared with controls (11% and 22%, respectively; P<0.05), and plaques of MΦLRP1 recipients were 13% smaller than those of wild-type recipients ( P<0.05). Recipients of MΦLRP1 marrow had 36% fewer M1 macrophages ( P<0.01) and 2.5-fold more CCR7 (C-C chemokine receptor type 7)-positive macrophages in the plaque relative to wild-type mice ( P<0.01). Additionally, in vivo studies of cellular egress showed a 4.6-fold increase in 5-ethynyl-2´-deoxyuridine-labeled CCR7 macrophages in mediastinal lymph nodes. Finally, in vivo studies of reverse cholesterol transport showed a 1.4-fold higher reverse cholesterol transport in MΦLRP1 recipient mice ( P<0.01).
CONCLUSIONS - Absence of macrophage low-density lipoprotein receptor-related protein 1 unexpectedly accelerates atherosclerosis regression, enhances reverse cholesterol transport, and increases expression of the motility receptor CCR7, which drives macrophage egress from lesions.
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21 MeSH Terms
BRAF and MEK inhibitor therapy eliminates Nestin-expressing melanoma cells in human tumors.
Doxie DB, Greenplate AR, Gandelman JS, Diggins KE, Roe CE, Dahlman KB, Sosman JA, Kelley MC, Irish JM
(2018) Pigment Cell Melanoma Res 31: 708-719
MeSH Terms: Antibodies, Neoplasm, Cell Line, Tumor, Humans, Imidazoles, Melanoma, Mitogen-Activated Protein Kinase Kinases, Nestin, Oximes, Phenotype, Protein Kinase Inhibitors, Proto-Oncogene Proteins B-raf, Pyridones, Pyrimidinones
Show Abstract · Added May 21, 2018
Little is known about the in vivo impacts of targeted therapy on melanoma cell abundance and protein expression. Here, 21 antibodies were added to an established melanoma mass cytometry panel to measure 32 cellular features, distinguish malignant cells, and characterize dabrafenib and trametinib responses in BRAF melanoma. Tumor cells were biopsied before neoadjuvant therapy and compared to cells surgically resected from the same site after 4 weeks of therapy. Approximately 50,000 cells per tumor were characterized by mass cytometry and computational tools t-SNE/viSNE, FlowSOM, and MEM. The resulting single-cell view of melanoma treatment response revealed initially heterogeneous melanoma tumors were consistently cleared of Nestin-expressing melanoma cells. Melanoma cell subsets that persisted to week 4 were heterogeneous but expressed SOX2 or SOX10 proteins and specifically lacked surface expression of MHC I proteins by MEM analysis. Traditional histology imaging of tissue microarrays from the same tumors confirmed mass cytometry results, including persistence of NES- SOX10+ S100β+ melanoma cells. This quantitative single-cell view of melanoma treatment response revealed protein features of malignant cells that are not eliminated by targeted therapy.
© 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
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13 MeSH Terms
Arrhythmia genetics: Not dark and lite, but 50 shades of gray.
Roden DM, Glazer AM, Kroncke B
(2018) Heart Rhythm 15: 1231-1232
MeSH Terms: Arrhythmias, Cardiac, Humans, Long QT Syndrome, Phenotype, Potassium Channels, Voltage-Gated
Added March 26, 2019
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High Frequency of Ovarian Cyst Development in Vhl;Snf5 Mice.
Kuwahara Y, Kennedy LM, Karnezis AN, Mora-Blanco EL, Rogers AB, Fletcher CD, Huntsman DG, Roberts CWM, Rathmell WK, Weissman BE
(2018) Am J Pathol 188: 1510-1516
MeSH Terms: Animals, Female, Hemorrhage, Mice, Mice, Knockout, Mutation, Ovarian Cysts, Phenotype, SMARCB1 Protein, Von Hippel-Lindau Tumor Suppressor Protein
Show Abstract · Added October 30, 2019
The new paradigm of mutations in chromatin-modifying genes as driver events in the development of cancers has proved challenging to resolve the complex influences over disease phenotypes. In particular, impaired activities of members of the SWI/SNF chromatin remodeling complex have appeared in an increasing variety of tumors. Mutations in SNF5, a member of this ubiquitously expressed complex, arise in almost all cases of malignant rhabdoid tumor in the absence of additional genetic alterations. Therefore, we studied how activation of additional oncogenic pathways might shift the phenotype of disease driven by SNF5 loss. With the use of a genetically engineered mouse model, we examined the effects of a hypomorphic Vhl allele on disease phenotype, with a modest up-regulation of the hypoxia response pathway. Snf5;Vhl mice did not demonstrate a substantial difference in overall survival or a change in malignant rhabdoid tumor development. However, a high percentage of female mice showed complex hemorrhagic ovarian cysts, a phenotype rarely found in either parental mouse strain. These lesions also showed mosaic expression of SNF5 by immunohistochemistry. Therefore, our studies implicate that modest changes in angiogenic regulation interact with perturbations of SWI/SNF complex activity to modulate disease phenotypes.
Copyright © 2018 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.
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Successful Establishment of Primary Type II Alveolar Epithelium with 3D Organotypic Coculture.
Sucre JMS, Jetter CS, Loomans H, Williams J, Plosa EJ, Benjamin JT, Young LR, Kropski JA, Calvi CL, Kook S, Wang P, Gleaves L, Eskaros A, Goetzl L, Blackwell TS, Guttentag SH, Zijlstra A
(2018) Am J Respir Cell Mol Biol 59: 158-166
MeSH Terms: Cell Communication, Cells, Cultured, Coculture Techniques, Epithelial Cells, Fibroblasts, Humans, Lung, Lung Injury, Phenotype
Show Abstract · Added April 1, 2019
Alveolar type II (AT2) epithelial cells are uniquely specialized to produce surfactant in the lung and act as progenitor cells in the process of repair after lung injury. AT2 cell injury has been implicated in several lung diseases, including idiopathic pulmonary fibrosis and bronchopulmonary dysplasia. The inability to maintain primary AT2 cells in culture has been a significant barrier in the investigation of pulmonary biology. We have addressed this knowledge gap by developing a three-dimensional (3D) organotypic coculture using primary human fetal AT2 cells and pulmonary fibroblasts. Grown on top of matrix-embedded fibroblasts, the primary human AT2 cells establish a monolayer and have direct contact with the underlying pulmonary fibroblasts. Unlike conventional two-dimensional (2D) culture, the structural and functional phenotype of the AT2 cells in our 3D organotypic culture was preserved over 7 days of culture, as evidenced by the presence of lamellar bodies and by production of surfactant proteins B and C. Importantly, the AT2 cells in 3D cocultures maintained the ability to replicate, with approximately 60% of AT2 cells staining positive for the proliferation marker Ki67, whereas no such proliferation is evident in 2D cultures of the same primary AT2 cells. This organotypic culture system enables interrogation of AT2 epithelial biology by providing a reductionist in vitro model in which to investigate the response of AT2 epithelial cells and AT2 cell-fibroblast interactions during lung injury and repair.
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9 MeSH Terms
The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma.
Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwiatkowski DJ, Lui W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WY, Robertson AG, Cancer Genome Atlas Research Network, Spellman PT, Rathmell WK, Linehan WM
(2018) Cell Rep 23: 313-326.e5
MeSH Terms: Biomarkers, Tumor, Carcinoma, Renal Cell, Cyclin-Dependent Kinase Inhibitor p16, Genome, Human, Humans, Kidney Neoplasms, Metabolic Networks and Pathways, Nuclear Proteins, PTEN Phosphohydrolase, Phenotype, Survival Analysis, Transcription Factors, Tumor Suppressor Proteins, Ubiquitin Thiolesterase
Show Abstract · Added October 30, 2019
Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival.
Published by Elsevier Inc.
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Precision Modeling of Pulmonary Hypertension Pathology with Induced Pluripotent Stem Cell-derived Cells.
West JD, Carrier EJ
(2018) Am J Respir Crit Care Med 198: 154-155
MeSH Terms: Bone Morphogenetic Protein Receptors, Type II, Humans, Hypertension, Hypertension, Pulmonary, Induced Pluripotent Stem Cells, Mutation, Phenotype
Added March 26, 2019
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7 MeSH Terms