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Fan Z, Ardicoglu R, Batavia AA, Rust R, von Ziegler L, Waag R, Zhang J, Desgeorges T, Sturman O, Dang H, Weber R, Roszkowski M, Moor AE, Schwab ME, Germain PL, Bohacek J, De Bock K. The vascular gene Apold1 is dispensable for normal development but controls angiogenesis under pathological conditions. Angiogenesis 2023; 26:385-407. [PMID: 36933174 PMCID: PMC10328887 DOI: 10.1007/s10456-023-09870-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/06/2023] [Indexed: 03/19/2023]
Abstract
The molecular mechanisms of angiogenesis have been intensely studied, but many genes that control endothelial behavior and fate still need to be described. Here, we characterize the role of Apold1 (Apolipoprotein L domain containing 1) in angiogenesis in vivo and in vitro. Single-cell analyses reveal that - across tissues - the expression of Apold1 is restricted to the vasculature and that Apold1 expression in endothelial cells (ECs) is highly sensitive to environmental factors. Using Apold1-/- mice, we find that Apold1 is dispensable for development and does not affect postnatal retinal angiogenesis nor alters the vascular network in adult brain and muscle. However, when exposed to ischemic conditions following photothrombotic stroke as well as femoral artery ligation, Apold1-/- mice display dramatic impairments in recovery and revascularization. We also find that human tumor endothelial cells express strikingly higher levels of Apold1 and that Apold1 deletion in mice stunts the growth of subcutaneous B16 melanoma tumors, which have smaller and poorly perfused vessels. Mechanistically, Apold1 is activated in ECs upon growth factor stimulation as well as in hypoxia, and Apold1 intrinsically controls EC proliferation but not migration. Our data demonstrate that Apold1 is a key regulator of angiogenesis in pathological settings, whereas it does not affect developmental angiogenesis, thus making it a promising candidate for clinical investigation.
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Affiliation(s)
- Zheng Fan
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
- Institute of Anatomy, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Raphaela Ardicoglu
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Aashil A Batavia
- Department of Pathology and Molecular Pathology, University and University Hospital Zürich, Zurich, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Ruslan Rust
- Department of Health Sciences and Technology, Institute for Regenerative Medicine, University of Zürich, ETH Zürich, Zurich, Switzerland
| | - Lukas von Ziegler
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Rebecca Waag
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Jing Zhang
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
| | - Thibaut Desgeorges
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
| | - Oliver Sturman
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Hairuo Dang
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
- DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Rebecca Weber
- Department of Health Sciences and Technology, Institute for Regenerative Medicine, University of Zürich, ETH Zürich, Zurich, Switzerland
| | - Martin Roszkowski
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Martin E Schwab
- Department of Health Sciences and Technology, Institute for Regenerative Medicine, University of Zürich, ETH Zürich, Zurich, Switzerland
| | - Pierre-Luc Germain
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
- Department of Health Sciences and Technology, Computational Neurogenomics, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Department for Molecular Life Sciences, Laboratory of Statistical Bioinformatics, University of Zürich, Zurich, Switzerland
| | - Johannes Bohacek
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland.
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland.
| | - Katrien De Bock
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland.
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2
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Stritt S, Nurden P, Nurden AT, Schved JF, Bordet JC, Roux M, Alessi MC, Trégouët DA, Mäkinen T, Giansily-Blaizot M. APOLD1 loss causes endothelial dysfunction involving cell junctions, cytoskeletal architecture, and Weibel-Palade bodies, while disrupting hemostasis. Haematologica 2023; 108:772-784. [PMID: 35638551 PMCID: PMC9973481 DOI: 10.3324/haematol.2022.280816] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Indexed: 11/09/2022] Open
Abstract
Vascular homeostasis is impaired in various diseases thereby contributing to the progression of their underlying pathologies. The endothelial immediate early gene Apolipoprotein L domain-containing 1 (APOLD1) helps to regulate endothelial function. However, its precise role in endothelial cell biology remains unclear. We have localized APOLD1 to endothelial cell contacts and to Weibel-Palade bodies (WPB) where it associates with von Willebrand factor (VWF) tubules. Silencing of APOLD1 in primary human endothelial cells disrupted the cell junction-cytoskeletal interface, thereby altering endothelial permeability accompanied by spontaneous release of WPB contents. This resulted in an increased presence of WPB cargoes, notably VWF and angiopoietin-2 in the extracellular medium. Autophagy flux, previously recognized as an essential mechanism for the regulated release of WPB, was impaired in the absence of APOLD1. In addition, we report APOLD1 as a candidate gene for a novel inherited bleeding disorder across three generations of a large family in which an atypical bleeding diathesis was associated with episodic impaired microcirculation. A dominant heterozygous nonsense APOLD1:p.R49* variant segregated to affected family members. Compromised vascular integrity resulting from an excess of plasma angiopoietin-2, and locally impaired availability of VWF may explain the unusual clinical profile of APOLD1:p.R49* patients. In summary, our findings identify APOLD1 as an important regulator of vascular homeostasis and raise the need to consider testing of endothelial cell function in patients with inherited bleeding disorders without apparent platelet or coagulation defects.
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Affiliation(s)
- Simon Stritt
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala
| | - Paquita Nurden
- Institut de Rythmologie et de Modélisation Cardiaque, Hôpital Xavier Arnozan, Pessac, France.
| | - Alan T Nurden
- Institut de Rythmologie et de Modélisation Cardiaque, Hôpital Xavier Arnozan, Pessac, France
| | - Jean-François Schved
- Department of Biological Hematology, CHU Montpellier, Université de Montpellier, Montpellier
| | - Jean-Claude Bordet
- Hematology, Hospices civils de Lyon, Bron biology center and Hemostasis- Thrombosis, Lyon-1 University, Lyon
| | | | | | - David-Alexandre Trégouët
- Laboratory of Excellence GENMED (Medical Genomics), Paris; University of Bordeaux, INSERM, Bordeaux Population Health Research Center, U1219, Bordeaux
| | - Taija Mäkinen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Muriel Giansily-Blaizot
- Department of Biological Hematology, CHU Montpellier, Université de Montpellier, Montpellier
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3
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Guo D, Zhang J, Han Y, Cui L, Wang H, Wang K, Li P, Deng R, Kang J, Duan Z. Transcriptomic Study on the Lungs of Broilers with Ascites Syndrome. Animals (Basel) 2023; 13:ani13010175. [PMID: 36611783 PMCID: PMC9817706 DOI: 10.3390/ani13010175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Although broiler ascites syndrome (AS) has been extensively studied, its pathogenesis remains unclear. The lack of cardiopulmonary function in broilers causes relative hypoxia in the body; hence, the lung is the main target organ of AS. However, the transcriptome of AS lung tissue in broilers has not been studied. In this study, an AS model was successfully constructed, and lung tissues of three AS broilers and three healthy broilers were obtained for RNA sequencing (RNA-seq) and pathological observation. The results showed that 614 genes were up-regulated and 828 genes were down-regulated in the AS group compared with the normal group. Gene Ontology (GO) functional annotation revealed the following up-regulated genes: FABP4, APLN, EIF2AK4, HMOX1, MMP9, THBS1, TLR4, BCL2; and down-regulated genes: APELA, FGF7, WNT5A, CDK6, IL7, IL7R, APLNR. These genes have attracted much attention in cardiovascular diseases such as pulmonary hypertension. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that multiple metabolic processes were enriched, indicating abnormal lung metabolism of AS in broilers. These findings elucidate the potential genes and signal pathways in the lungs of broilers with AS and provide a potential target for studying the pathogenesis and preventing AS.
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Hernández Cordero AI, Yang CX, Yang J, Horvath S, Shaipanich T, MacIsaac J, Lin DTS, Kobor MS, Guillemi S, Harris M, Lam W, Lam S, Montaner J, Man SFP, Sin DD, Leung JM. Airway Aging and Methylation Disruptions in HIV-associated Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2022; 206:150-160. [PMID: 35426765 PMCID: PMC9887412 DOI: 10.1164/rccm.202106-1440oc] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Rationale: Age-related diseases like chronic obstructive pulmonary disease (COPD) occur at higher rates in people living with human immunodeficiency virus (PLWH) than in uninfected populations. Objectives: To identify whether accelerated aging can be observed in the airways of PLWH with COPD, manifest by a unique DNA methylation signature. Methods: Bronchial epithelial brushings from PLWH with and without COPD and HIV-uninfected adults with and without COPD (N = 76) were profiled for DNA methylation and gene expression. We evaluated global Alu and LINE-1 methylation and calculated the epigenetic age using the Horvath clock and the methylation telomere length estimator. To identify genome-wide differential DNA methylation and gene expression associated with HIV and COPD, robust linear models were used followed by an expression quantitative trait methylation (eQTM) analysis. Measurements and Main Results: Epigenetic age acceleration and shorter methylation estimates of telomere length were found in PLWH with COPD compared with PLWH without COPD and uninfected patients with and without COPD. Global hypomethylation was identified in PLWH. We identified 7,970 cytosine bases located next to a guanine base (CpG sites), 293 genes, and 9 expression quantitative trait methylation-gene pairs associated with the interaction between HIV and COPD. Actin binding LIM protein family member 3 (ABLIM3) was one of the novel candidate genes for HIV-associated COPD highlighted by our analysis. Conclusions: Methylation age acceleration is observed in the airway epithelium of PLWH with COPD, a process that may be responsible for the heightened risk of COPD in this population. Their distinct methylation profile, differing from that observed in patients with COPD alone, suggests a unique pathogenesis to HIV-associated COPD. The associations warrant further investigation to establish causality.
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Affiliation(s)
- Ana I. Hernández Cordero
- Centre for Heart Lung Innovation, St. Paul’s Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Chen Xi Yang
- Centre for Heart Lung Innovation, St. Paul’s Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia Yang
- Centre for Heart Lung Innovation, St. Paul’s Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, California;,Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | | | | | | | | | - Silvia Guillemi
- Faculty of Medicine, and,British Columbia Centre for Excellence in HIV/AIDS, Providence Health Care, Vancouver, British Columbia, Canada
| | - Marianne Harris
- Faculty of Medicine, and,British Columbia Centre for Excellence in HIV/AIDS, Providence Health Care, Vancouver, British Columbia, Canada
| | - Wan Lam
- British Columbia Cancer, University of British Columbia, Vancouver, British Columbia, Canada; and
| | | | - Julio Montaner
- Faculty of Medicine, and,British Columbia Centre for Excellence in HIV/AIDS, Providence Health Care, Vancouver, British Columbia, Canada
| | - S. F. Paul Man
- Centre for Heart Lung Innovation, St. Paul’s Hospital and University of British Columbia, Vancouver, British Columbia, Canada;,Division of Respiratory Medicine, Department of Medicine
| | - Don D. Sin
- Centre for Heart Lung Innovation, St. Paul’s Hospital and University of British Columbia, Vancouver, British Columbia, Canada;,Division of Respiratory Medicine, Department of Medicine
| | - Janice M. Leung
- Centre for Heart Lung Innovation, St. Paul’s Hospital and University of British Columbia, Vancouver, British Columbia, Canada;,Division of Respiratory Medicine, Department of Medicine
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5
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Yee M, Cohen ED, Domm W, Porter GA, McDavid AN, O’Reilly MA. Neonatal hyperoxia depletes pulmonary vein cardiomyocytes in adult mice via mitochondrial oxidation. Am J Physiol Lung Cell Mol Physiol 2018; 314:L846-L859. [PMID: 29345197 PMCID: PMC6008126 DOI: 10.1152/ajplung.00409.2017] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Supplemental oxygen given to preterm infants has been associated with permanently altering postnatal lung development. Now that these individuals are reaching adulthood, there is growing concern that early life oxygen exposure may also promote cardiovascular disease through poorly understood mechanisms. We previously reported that adult mice exposed to 100% oxygen between postnatal days 0 and 4 develop pulmonary hypertension, defined pathologically by capillary rarefaction, dilation of arterioles and veins, cardiac failure, and a reduced lifespan. Here, Affymetrix Gene Arrays are used to identify early transcriptional changes that take place in the lung before pulmonary capillary rarefaction. We discovered neonatal hyperoxia reduced expression of cardiac muscle genes, including those involved in contraction, calcium signaling, mitochondrial respiration, and vasodilation. Quantitative RT-PCR, immunohistochemistry, and genetic lineage mapping using Myh6CreER; Rosa26RmT/mG mice revealed this reflected loss of pulmonary vein cardiomyocytes. The greatest loss of cadiomyocytes was seen within the lung followed by a graded loss beginning at the hilum and extending into the left atrium. Loss of these cells was seen by 2 wk of age in mice exposed to ≥80% oxygen and was attributed, in part, to reduced proliferation. Administering mitoTEMPO, a scavenger of mitochondrial superoxide during neonatal hyperoxia prevented loss of these cells. Since pulmonary vein cardiomyocytes help pump oxygen-rich blood out of the lung, their early loss following neonatal hyperoxia may contribute to cardiovascular disease seen in these mice, and perhaps in people who were born preterm.
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Affiliation(s)
- Min Yee
- 1Department of Pediatrics, School of Medicine and Dentistry, The University of Rochester, Rochester, New York
| | - Ethan David Cohen
- 2Department of Medicine, School of Medicine and Dentistry, The University of Rochester, Rochester, New York
| | - William Domm
- 1Department of Pediatrics, School of Medicine and Dentistry, The University of Rochester, Rochester, New York
| | - George A. Porter
- 1Department of Pediatrics, School of Medicine and Dentistry, The University of Rochester, Rochester, New York
| | - Andrew N. McDavid
- 3Biostatistics and Computational Biology, School of Medicine and Dentistry, The University of Rochester, Rochester, New York
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6
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Scumpia PO, Botten GA, Norman JS, Kelly-Scumpia KM, Spreafico R, Ruccia AR, Purbey PK, Thomas BJ, Modlin RL, Smale ST. Opposing roles of Toll-like receptor and cytosolic DNA-STING signaling pathways for Staphylococcus aureus cutaneous host defense. PLoS Pathog 2017; 13:e1006496. [PMID: 28704551 PMCID: PMC5526579 DOI: 10.1371/journal.ppat.1006496] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/25/2017] [Accepted: 06/27/2017] [Indexed: 01/01/2023] Open
Abstract
Successful host defense against pathogens requires innate immune recognition of the correct pathogen associated molecular patterns (PAMPs) by pathogen recognition receptors (PRRs) to trigger the appropriate gene program tailored to the pathogen. While many PRR pathways contribute to the innate immune response to specific pathogens, the relative importance of each pathway for the complete transcriptional program elicited has not been examined in detail. Herein, we used RNA-sequencing with wildtype and mutant macrophages to delineate the innate immune pathways contributing to the early transcriptional response to Staphylococcus aureus, a ubiquitous microorganism that can activate a wide variety of PRRs. Unexpectedly, two PRR pathways—the Toll-like receptor (TLR) and Stimulator of Interferon Gene (STING) pathways—were identified as dominant regulators of approximately 95% of the genes that were potently induced within the first four hours of macrophage infection with live S. aureus. TLR signaling predominantly activated a pro-inflammatory program while STING signaling activated an antiviral/type I interferon response with live but not killed S. aureus. This STING response was largely dependent on the cytosolic DNA sensor cyclic guanosine-adenosine synthase (cGAS). Using a cutaneous infection model, we found that the TLR and STING pathways played opposite roles in host defense to S. aureus. TLR signaling was required for host defense, with its absence reducing interleukin (IL)-1β production and neutrophil recruitment, resulting in increased bacterial growth. In contrast, absence of STING signaling had the opposite effect, enhancing the ability to restrict the infection. These results provide novel insights into the complex interplay of innate immune signaling pathways triggered by S. aureus and uncover opposing roles of TLR and STING in cutaneous host defense to S. aureus. Individual pathogen associated molecular patterns (PAMPs) induce gene expression in immune cells through distinct signaling pathways to protect cells from infection. However, pathogens typically possess many PAMPs, and the precise contribution of each PAMP to the gene expression program elicited by a live pathogen has not been clearly defined. Herein, we used gene expression profiling to examine the full early response of macrophages to Staphylococcus aureus, a major human opportunistic pathogen. Surprisingly, we found that two pathogen-sensing pathways, Toll-like receptor (TLR) and Stimulator of Interferon Signaling Gene (STING) pathways, contribute to the activation of ~95% of the genes induced by S. aureus infection. The remaining genes may be induced by hypoxia pathways. When the bacterium is dead, 98% of the gene induction occurs through TLR signaling, and neither STING nor hypoxia contributes greatly to the response. STING activation requires sensing of S. aureus DNA by the cytosolic DNA sensor, cGAS. During S. aureus skin infection, the TLR and STING pathways compete with each other to induce or suppress host defense, respectively, by counter regulating interleukin 1β production and neutrophil recruitment. A similar approach may allow delineation of the relative contributions of immune pathways in the response to various live pathogens.
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Affiliation(s)
- Philip O Scumpia
- Department of Medicine, Division of Dermatology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Giovanni A Botten
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Joshua S Norman
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Kindra M Kelly-Scumpia
- Department of Medicine, Division of Dermatology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Roberto Spreafico
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California, United States of America.,Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Amber R Ruccia
- Department of Medicine, Division of Dermatology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Prabhat K Purbey
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Brandon J Thomas
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Robert L Modlin
- Department of Medicine, Division of Dermatology, University of California at Los Angeles, Los Angeles, California, United States of America.,Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Stephen T Smale
- Department of Microbiology, Immunology, and Molecular Genetics, University of California at Los Angeles, Los Angeles, California, United States of America
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7
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Hu H, Petousi N, Glusman G, Yu Y, Bohlender R, Tashi T, Downie JM, Roach JC, Cole AM, Lorenzo FR, Rogers AR, Brunkow ME, Cavalleri G, Hood L, Alpatty SM, Prchal JT, Jorde LB, Robbins PA, Simonson TS, Huff CD. Evolutionary history of Tibetans inferred from whole-genome sequencing. PLoS Genet 2017; 13:e1006675. [PMID: 28448578 PMCID: PMC5407610 DOI: 10.1371/journal.pgen.1006675] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 03/08/2017] [Indexed: 12/20/2022] Open
Abstract
The indigenous people of the Tibetan Plateau have been the subject of much recent interest because of their unique genetic adaptations to high altitude. Recent studies have demonstrated that the Tibetan EPAS1 haplotype is involved in high altitude-adaptation and originated in an archaic Denisovan-related population. We sequenced the whole-genomes of 27 Tibetans and conducted analyses to infer a detailed history of demography and natural selection of this population. We detected evidence of population structure between the ancestral Han and Tibetan subpopulations as early as 44 to 58 thousand years ago, but with high rates of gene flow until approximately 9 thousand years ago. The CMS test ranked EPAS1 and EGLN1 as the top two positive selection candidates, and in addition identified PTGIS, VDR, and KCTD12 as new candidate genes. The advantageous Tibetan EPAS1 haplotype shared many variants with the Denisovan genome, with an ancient gene tree divergence between the Tibetan and Denisovan haplotypes of about 1 million years ago. With the exception of EPAS1, we observed no evidence of positive selection on Denisovan-like haplotypes.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Nayia Petousi
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gustavo Glusman
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Yao Yu
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ryan Bohlender
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Tsewang Tashi
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
| | - Jonathan M. Downie
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Amy M. Cole
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Felipe R. Lorenzo
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
| | - Alan R. Rogers
- Department of Anthropology, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary E. Brunkow
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Gianpiero Cavalleri
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Sama M. Alpatty
- Skaggs School of Pharmacy and Pharmaceutical Science, UC San Diego, La Jolla, California, United States of America
| | - Josef T. Prchal
- Department of Medicine, University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt Lake City, Utah, United States of America
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Peter A. Robbins
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Tatum S. Simonson
- Department of Medicine, Division of Physiology, University of California San Diego, La Jolla, California, United States of America
| | - Chad D. Huff
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
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8
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Chen T, Yang C, Li M, Tan X. Alveolar Hypoxia-Induced Pulmonary Inflammation: From Local Initiation to Secondary Promotion by Activated Systemic Inflammation. J Vasc Res 2016; 53:317-329. [PMID: 27974708 DOI: 10.1159/000452800] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 10/23/2016] [Indexed: 11/19/2022] Open
Abstract
Pulmonary hypertension (PH) is a pathological condition with high mortality and morbidity. Hypoxic PH (HPH) is a common form of PH occurring mainly due to lung disease and/or hypoxia. Most causes of HPH are associated with persistent or intermittent alveolar hypoxia, including exposure to high altitude and chronic obstructive respiratory disease. Recent evidence suggests that inflammation is a critical step for HPH initiation and development. A detailed understanding of the initiation and progression of pulmonary inflammation would help in exploring potential clinical treatments for HPH. In this review, the mechanism for alveolar hypoxia-induced local lung inflammation and its progression are discussed as follows: (1) low alveolar PO2 levels activate resident lung cells, mainly the alveolar macrophages, which initiate pulmonary inflammation; (2) systemic inflammation is induced by alveolar hypoxia through alveolar macrophage activation; (3) monocytes are recruited into the pulmonary circulation by alveolar hypoxia-induced macrophage activation, which then contributes to the progression of pulmonary inflammation during the chronic phase of alveolar hypoxia, and (4) alveolar hypoxia-induced systemic inflammation contributes to the development of HPH. We hypothesize that a combination of alveolar hypoxia-induced local lung inflammation and the initiation of systemic inflammation ("second hit") is essential for HPH progression.
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Affiliation(s)
- Ting Chen
- Department of High Altitude Physiology and Biology, College of High Altitude Medicine, Third Military Medical University, Ministry of Education, Chongqing, China
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9
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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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