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Abbey CA, Duran CL, Chen Z, Chen Y, Roy S, Coffell A, Sveeggen TM, Chakraborty S, Wells GB, Chang J, Bayless KJ. Identification of New Markers of Angiogenic Sprouting Using Transcriptomics: New Role for RND3. Arterioscler Thromb Vasc Biol 2024; 44:e145-e167. [PMID: 38482696 PMCID: PMC11043006 DOI: 10.1161/atvbaha.123.320599] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/28/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND New blood vessel formation requires endothelial cells to transition from a quiescent to an invasive phenotype. Transcriptional changes are vital for this switch, but a comprehensive genome-wide approach focused exclusively on endothelial cell sprout initiation has not been reported. METHODS Using a model of human endothelial cell sprout initiation, we developed a protocol to physically separate cells that initiate the process of new blood vessel formation (invading cells) from noninvading cells. We used this model to perform multiple transcriptomics analyses from independent donors to monitor endothelial gene expression changes. RESULTS Single-cell population analyses, single-cell cluster analyses, and bulk RNA sequencing revealed common transcriptomic changes associated with invading cells. We also found that collagenase digestion used to isolate single cells upregulated the Fos proto-oncogene transcription factor. Exclusion of Fos proto-oncogene expressing cells revealed a gene signature consistent with activation of signal transduction, morphogenesis, and immune responses. Many of the genes were previously shown to regulate angiogenesis and included multiple tip cell markers. Upregulation of SNAI1 (snail family transcriptional repressor 1), PTGS2 (prostaglandin synthase 2), and JUNB (JunB proto-oncogene) protein expression was confirmed in invading cells, and silencing JunB and SNAI1 significantly reduced invasion responses. Separate studies investigated rounding 3, also known as RhoE, which has not yet been implicated in angiogenesis. Silencing rounding 3 reduced endothelial invasion distance as well as filopodia length, fitting with a pathfinding role for rounding 3 via regulation of filopodial extensions. Analysis of in vivo retinal angiogenesis in Rnd3 heterozygous mice confirmed a decrease in filopodial length compared with wild-type littermates. CONCLUSIONS Validation of multiple genes, including rounding 3, revealed a functional role for this gene signature early in the angiogenic process. This study expands the list of genes associated with the acquisition of a tip cell phenotype during endothelial cell sprout initiation.
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Affiliation(s)
- Colette A. Abbey
- Texas A&M Health, Department of Medical Physiology, Texas A&M School of Medicine, Bryan TX
- Department of Molecular & Cellular Medicine, Texas A&M School of Medicine, Bryan, TX
| | - Camille L. Duran
- Department of Molecular & Cellular Medicine, Texas A&M School of Medicine, Bryan, TX
| | - Zhishi Chen
- Center for Genomic and Precision Medicine, Institute of Biosciences and Technology, Houston, TX
| | - Yanping Chen
- Center for Genomic and Precision Medicine, Institute of Biosciences and Technology, Houston, TX
| | - Sukanya Roy
- Texas A&M Health, Department of Medical Physiology, Texas A&M School of Medicine, Bryan TX
| | - Ashley Coffell
- Department of Molecular & Cellular Medicine, Texas A&M School of Medicine, Bryan, TX
| | - Timothy M. Sveeggen
- Department of Molecular & Cellular Medicine, Texas A&M School of Medicine, Bryan, TX
| | - Sanjukta Chakraborty
- Texas A&M Health, Department of Medical Physiology, Texas A&M School of Medicine, Bryan TX
| | - Gregg B. Wells
- Department of Molecular & Cellular Medicine, Texas A&M School of Medicine, Bryan, TX
- Department of Cell Biology and Genetics, Texas A&M School of Medicine, Bryan, TX
| | - Jiang Chang
- Center for Genomic and Precision Medicine, Institute of Biosciences and Technology, Houston, TX
| | - Kayla J. Bayless
- Texas A&M Health, Department of Medical Physiology, Texas A&M School of Medicine, Bryan TX
- Department of Molecular & Cellular Medicine, Texas A&M School of Medicine, Bryan, TX
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Kuihon SVNP, Sevart BJ, Abbey CA, Bayless KJ, Chen B. The NADPH oxidase 2 subunit p47 phox binds to the WAVE regulatory complex and p22 phox in a mutually exclusive manner. J Biol Chem 2024; 300:107130. [PMID: 38432630 PMCID: PMC10979099 DOI: 10.1016/j.jbc.2024.107130] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/15/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024] Open
Abstract
The actin cytoskeleton and reactive oxygen species (ROS) both play crucial roles in various cellular processes. Previous research indicated a direct interaction between two key components of these systems: the WAVE1 subunit of the WAVE regulatory complex (WRC), which promotes actin polymerization and the p47phox subunit of the NADPH oxidase 2 complex (NOX2), which produces ROS. Here, using carefully characterized recombinant proteins, we find that activated p47phox uses its dual Src homology 3 domains to bind to multiple regions within the WAVE1 and Abi2 subunits of the WRC, without altering WRC's activity in promoting Arp2/3-mediated actin polymerization. Notably, contrary to previous findings, p47phox uses the same binding pocket to interact with both the WRC and the p22phox subunit of NOX2, albeit in a mutually exclusive manner. This observation suggests that when activated, p47phox may separately participate in two distinct processes: assembling into NOX2 to promote ROS production and engaging with WRC to regulate the actin cytoskeleton.
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Affiliation(s)
- Simon V N P Kuihon
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Brodrick J Sevart
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Colette A Abbey
- Department of Medical Physiology, Texas A&M Health Science Center, Bryan, Texas, USA
| | - Kayla J Bayless
- Department of Medical Physiology, Texas A&M Health Science Center, Bryan, Texas, USA
| | - Baoyu Chen
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa, USA.
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Sveeggen TM, Abbey CA, Smith RL, Salinas ML, Chapkin RS, Bayless KJ. Annexin A2 modulates phospholipid membrane composition upstream of Arp2 to control angiogenic sprout initiation. FASEB J 2023; 37:e22715. [PMID: 36527391 PMCID: PMC10586062 DOI: 10.1096/fj.202201088r] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/10/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
The intersection of protein and lipid biology is of growing importance for understanding how cells address structural challenges during adhesion and migration. While protein complexes engaged with the cytoskeleton play a vital role, support from the phospholipid membrane is crucial for directing localization and assembly of key protein complexes. During angiogenesis, dramatic cellular remodeling is necessary for endothelial cells to shift from a stable monolayer to invasive structures. However, the molecular dynamics between lipids and proteins during endothelial invasion are not defined. Here, we utilized cell culture, immunofluorescence, and lipidomic analyses to identify a novel role for the membrane binding protein Annexin A2 (ANXA2) in modulating the composition of specific membrane lipids necessary for cortical F-actin organization and adherens junction stabilization. In the absence of ANXA2, there is disorganized cortical F-actin, reduced junctional Arp2, excess sprout initiation, and ultimately failed sprout maturation. Furthermore, we observed reduced filipin III labeling of membrane cholesterol in cells with reduced ANXA2, suggesting there is an alteration in phospholipid membrane dynamics. Lipidomic analyses revealed that 42 lipid species were altered with loss of ANXA2, including an accumulation of phosphatidylcholine (16:0_16:0). We found that supplementation of phosphatidylcholine (16:0_16:0) in wild-type endothelial cells mimicked the ANXA2 knock-down phenotype, indicating that ANXA2 regulated the phospholipid membrane upstream of Arp2 recruitment and organization of cortical F-actin. Altogether, these data indicate a novel role for ANXA2 in coordinating events at endothelial junctions needed to initiate sprouting and show that proper lipid modulation is a critical component of these events.
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Affiliation(s)
- Timothy M. Sveeggen
- Texas A&M Health Science Center, Texas, Bryan, USA
- Interdisciplinary Graduate Program in Genetics, Texas A&M University, College Station, Texas, USA
| | | | | | - Michael L. Salinas
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, Texas, USA
- Department of Nutrition, Texas A&M University, College Station, Texas, USA
| | - Robert S. Chapkin
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, Texas, USA
- Department of Nutrition, Texas A&M University, College Station, Texas, USA
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Kumaravel S, Abbey CA, Bayless KJ, Chakraborty S. The β 1-integrin plays a key role in LEC invasion in an optimized 3-D collagen matrix model. Am J Physiol Cell Physiol 2020; 319:C1045-C1058. [PMID: 33052069 DOI: 10.1152/ajpcell.00299.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Lymphangiogenesis, or formation of new lymphatic vessels, is a tightly regulated process that is controlled by growth factor signaling and biomechanical cues. Lymphatic endothelial cells (LECs) undergo remodeling, migration, and proliferation to invade the surrounding extracellular matrix (ECM) during both physiological and pathological lymphangiogenesis. This study optimized conditions for an in vitro three-dimensional (3-D) collagen-based model that induced LEC invasion and recapitulated physiological formation of lymphatic capillaries with lumens. Invasion of LECs was enhanced in the presence of sphingosine 1-phosphate (S1P). Effects of various known lymphangiogenic factors, vascular endothelial growth factor (VEGF)-A, basic fibroblast growth factor (bFGF), interleukin (IL)-8, and hepatocyte growth factor (HGF), were tested on LEC sprout formation synergistically with VEGF-C. Several of these growth factors significantly enhanced LEC invasion, and synergistic effects of some of these further enhanced the sprouting density and lumen volume. To determine the contribution of specific ECM components, we analyzed the expression of different integrin subunits. Basal expressions of the integrin α5- and integrin β1-subunits were high in LECs. The addition of fibronectin, which mediates cellular responses through these integrins, enhanced LEC sprouting density and sprout length dose-dependently. siRNA-mediated knockdown of the integrin β1-subunit suppressed LEC invasion and also inhibited VEGF receptor (VEGFR)3 and ERK activation. Furthermore, exposing LECs to the inflammatory mediator lipopolysaccharide (LPS) inhibited sprouting. This optimized model for LEC invasion includes S1P, VEGF-C, and fibronectin within a 3-D collagen matrix, along with VEGF-C, VEGF-A, bFGF, and HGF in the culture medium, and provides a useful tool to investigate the functional effect of various lymphangiogenic factors and inhibitors.
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Affiliation(s)
- Subhashree Kumaravel
- Department of Medical Physiology, Texas A&M Health Science Center, College of Medicine, Bryan, Texas
| | - Colette A Abbey
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, Bryan, Texas
| | - Kayla J Bayless
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, Bryan, Texas
| | - Sanjukta Chakraborty
- Department of Medical Physiology, Texas A&M Health Science Center, College of Medicine, Bryan, Texas
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Shi L, Zhao M, Abbey CA, Tsai SH, Xie W, Pham D, Chapman S, Bayless KJ, Hein TW, Rosa RH, Ko ML, Kuo L, Ko GYP. Newly Identified Peptide, Peptide Lv, Promotes Pathological Angiogenesis. J Am Heart Assoc 2019; 8:e013673. [PMID: 31698979 PMCID: PMC6915261 DOI: 10.1161/jaha.119.013673] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background We recently discovered a small endogenous peptide, peptide Lv, with the ability to activate vascular endothelial growth factor receptor 2 and its downstream signaling. As vascular endothelial growth factor through vascular endothelial growth factor receptor 2 contributes to normal development, vasodilation, angiogenesis, and pathogenesis of various diseases, we investigated the role of peptide Lv in vasodilation and developmental and pathological angiogenesis in this study. Methods and Results The endothelial cell proliferation, migration, and 3-dimensional sprouting assays were used to test the abilities of peptide Lv in angiogenesis in vitro. The chick chorioallantoic membranes and early postnatal mice were used to examine its impact on developmental angiogenesis. The oxygen-induced retinopathy and laser-induced choroidal neovascularization mouse models were used for in vivo pathological angiogenesis. The isolated porcine retinal and coronary arterioles were used for vasodilation assays. Peptide Lv elicited angiogenesis in vitro and in vivo. Peptide Lv and vascular endothelial growth factor acted synergistically in promoting endothelial cell proliferation. Peptide Lv-elicited vasodilation was not completely dependent on nitric oxide, indicating that peptide Lv had vascular endothelial growth factor receptor 2/nitric oxide-independent targets. An antibody against peptide Lv, anti-Lv, dampened vascular endothelial growth factor-elicited endothelial proliferation and laser-induced vascular leakage and choroidal neovascularization. While the pathological angiogenesis in mouse eyes with oxygen-induced retinopathy was enhanced by exogenous peptide Lv, anti-Lv dampened this process. Furthermore, deletion of peptide Lv in mice significantly decreased pathological neovascularization compared with their wild-type littermates. Conclusions These results demonstrate that peptide Lv plays a significant role in pathological angiogenesis but may be less critical during development. Peptide Lv is involved in pathological angiogenesis through vascular endothelial growth factor receptor 2-dependent and -independent pathways. As anti-Lv dampened the pathological angiogenesis in the eye, anti-Lv may have a therapeutic potential to treat pathological angiogenesis.
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Affiliation(s)
- Liheng Shi
- Department of Veterinary Integrative Biosciences College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station TX
| | - Min Zhao
- Department of Medical Physiology Ophthalmic Vascular Research Program College of Medicine Texas A&M University Health Science Center Bryan TX
| | - Colette A Abbey
- Department of Molecular and Cellular Medicine College of Medicine Texas A&M University Health Science Center Bryan TX
| | - Shu-Huai Tsai
- Department of Medical Physiology Ophthalmic Vascular Research Program College of Medicine Texas A&M University Health Science Center Bryan TX
| | - Wankun Xie
- Department of Medical Physiology Ophthalmic Vascular Research Program College of Medicine Texas A&M University Health Science Center Bryan TX
| | - Dylan Pham
- Department of Veterinary Integrative Biosciences College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station TX
| | - Samantha Chapman
- Department of Veterinary Integrative Biosciences College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station TX
| | - Kayla J Bayless
- Department of Molecular and Cellular Medicine College of Medicine Texas A&M University Health Science Center Bryan TX
| | - Travis W Hein
- Department of Medical Physiology Ophthalmic Vascular Research Program College of Medicine Texas A&M University Health Science Center Bryan TX
| | - Robert H Rosa
- Department of Medical Physiology Ophthalmic Vascular Research Program College of Medicine Texas A&M University Health Science Center Bryan TX.,Department of Ophthalmology Baylor Scott & White Eye Institute Temple TX
| | - Michael L Ko
- Department of Veterinary Integrative Biosciences College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station TX.,Department of Biology Blinn College Bryan TX
| | - Lih Kuo
- Department of Medical Physiology Ophthalmic Vascular Research Program College of Medicine Texas A&M University Health Science Center Bryan TX
| | - Gladys Y-P Ko
- Department of Veterinary Integrative Biosciences College of Veterinary Medicine and Biomedical Sciences Texas A&M University College Station TX.,Texas A&M Institute for Neuroscience Texas A&M University College Station TX
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Bayless K, Duran CL, Abbey CA, Kang HA. Assembly of a mechanosensitive complex is required to initiate sprouting angiogenesis. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.83.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kayla Bayless
- Molecular & Cellular MedicineTexas A and M University Department of Molecular and Cellular MedicineCollege StationTX
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Duran CL, Abbey CA, Bayless KJ. Establishment of a three-dimensional model to study human uterine angiogenesis. Mol Hum Reprod 2019; 24:74-93. [PMID: 29329415 DOI: 10.1093/molehr/gax064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 12/19/2017] [Indexed: 01/29/2023] Open
Abstract
STUDY QUESTION Can primary human uterine microvascular endothelial cells (UtMVECs) be used as a model to study uterine angiogenic responses in vitro that are relevant in pregnancy? SUMMARY ANSWER UtMVECs demonstrated angiogenic responses when stimulated with proangiogenic factors, including sphingosine 1-phosphate (S1P), vascular endothelial growth factor (VEGF), basic fibroblast growth factor (bFGF), physiological levels of wall shear stress (WSS), human chorionic gonadotropin (hCG) and various combinations of estrogen and progesterone. WHAT IS KNOWN ALREADY During sprouting angiogenesis, signaling from growth factors and cytokines induces a monolayer of quiescent endothelial cells (ECs) lining the vasculature to degrade the extracellular matrix and invade the surrounding tissue to form new capillaries. During pregnancy and the female reproductive cycle, the uterine endothelium becomes activated and undergoes sprouting angiogenesis to increase the size and number of blood vessels in the endometrium. STUDY DESIGN, SIZE, DURATION The study was designed to examine the angiogenic potential of primary human UtMVECs using the well-characterized human umbilical vein EC (HUVEC) line as a control to compare angiogenic potential. ECs were seeded onto three-dimensional (3D) collagen matrices, supplemented with known proangiogenic stimuli relevant to pregnancy and allowed to invade for 24 h. Sprouting responses were analyzed using manual and automated methods for quantification. PARTICIPANTS/MATERIALS, SETTING, METHODS RT-PCR, Western blot analysis and immunostaining were used to characterize UtMVECs. Angiogenic responses were examined using 3D invasion assays. Western blotting was used to confirm signaling responses after proangiogenic lipid, pharmacological inhibitor, and recombinant lentiviral treatments. All experiments were repeated at least three times. MAIN RESULTS AND THE ROLE OF CHANCE After ensuring that UtMVECs expressed the proper endothelial markers, we found that UtMVECs invade 3D collagen matrices dose-dependently in response to known proangiogenic stimuli (e.g. S1P, VEGF, bFGF, hCG, estrogen, progesterone and WSS) present during early pregnancy. Invasion responses were positively correlated with phosphorylation of phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt) and p42/p44 mitogen-activated protein kinase (ERK). Inhibition of these second messengers significantly impaired sprouting (P < 0.01). Gene silencing of membrane type 1-matrix metalloproteinase using multiple approaches completely abrogated sprouting (P < 0.001). Finally, UtMVECs displayed a unique ability to undergo sprouting in response to hCG, and combined estrogen and progesterone treatment. LARGE SCALE DATA Not applicable. LIMITATIONS, REASONS FOR CAUTION The study of uterine angiogenesis in vitro has limitations and any findings many not fully represent the in vivo state. However, these experiments do provide evidence for the ability of UtMVECs to be used in functional sprouting assays in a 3D environment, stimulated by physiological factors that are produced locally within the uterus during early pregnancy. WIDER IMPLICATIONS OF THE FINDINGS We show that UtMVECs can be used reliably to investigate how growth factors, hormones, lipids and other factors, such as flow, affect angiogenesis in the uterus. STUDY FUNDING/COMPETING INTERESTS This work was supported by NIH award HL095786 to K.J.B. The authors have no conflicts of interest.
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Affiliation(s)
- Camille L Duran
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, 440 Reynolds Medical Building, College Station, TX 77843-1114, USA.,Interdisciplinary Program in Genetics, Texas A&M University, Mail Stop 2128, College Station, TX 77843, USA
| | - Colette A Abbey
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, 440 Reynolds Medical Building, College Station, TX 77843-1114, USA
| | - Kayla J Bayless
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, 440 Reynolds Medical Building, College Station, TX 77843-1114, USA.,Interdisciplinary Program in Genetics, Texas A&M University, Mail Stop 2128, College Station, TX 77843, USA.,Interdisciplinary Faculty of Reproductive Biology, Texas A&M University, Mail Stop 2471, College Station, TX 77843, USA
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Dave JM, Abbey CA, Duran CL, Seo H, Johnson GA, Bayless KJ. Hic-5 mediates the initiation of endothelial sprouting by regulating a key surface metalloproteinase. J Cell Sci 2016; 129:743-56. [PMID: 26769900 DOI: 10.1242/jcs.170571] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 01/05/2016] [Indexed: 12/16/2022] Open
Abstract
During angiogenesis, endothelial cells must coordinate matrix proteolysis with migration. Here, we tested whether the focal adhesion scaffold protein Hic-5 (also known as TGFB1I1) regulated endothelial sprouting in three dimensions. Hic-5 silencing reduced endothelial sprouting and lumen formation, and sprouting defects were rescued by the return of Hic-5 expression. Pro-angiogenic factors enhanced colocalization and complex formation between membrane type-1 matrix metalloproteinase (MT1-MMP, also known as MMP14) and Hic-5, but not between paxillin and MT1-MMP. The LIM2 and LIM3 domains of Hic-5 were necessary and sufficient for Hic-5 to form a complex with MT1-MMP. The degree of interaction between MT1-MMP and Hic-5 and the localization of the complex within detergent-resistant membrane fractions were enhanced during endothelial sprouting, and Hic-5 depletion lowered the surface levels of MT1-MMP. In addition, we observed that loss of Hic-5 partially reduced complex formation between MT1-MMP and focal adhesion kinase (FAK, also known as PTK2), suggesting that Hic-5 bridges MT1-MMP and FAK. Finally, Hic-5 LIM2-LIM3 deletion mutants reduced sprout initiation. Hic-5, MT1-MMP and FAK colocalized in angiogenic vessels during porcine pregnancy, supporting that this complex assembles during angiogenesis in vivo. Collectively, Hic-5 appears to enhance complex formation between MT1-MMP and FAK in activated endothelial cells, which likely coordinates matrix proteolysis and cell motility.
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Affiliation(s)
- Jui M Dave
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
| | - Colette A Abbey
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
| | - Camille L Duran
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
| | - Heewon Seo
- Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Gregory A Johnson
- Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Kayla J Bayless
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843, USA
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Kang H, Duran CL, Abbey CA, Kaunas RR, Bayless KJ. Fluid shear stress promotes proprotein convertase-dependent activation of MT1-MMP. Biochem Biophys Res Commun 2015; 460:596-602. [PMID: 25800869 DOI: 10.1016/j.bbrc.2015.03.075] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 03/13/2015] [Indexed: 11/26/2022]
Abstract
During angiogenesis, endothelial cells (ECs(1)) initiate new blood vessel growth and invade into the extracellular matrix (ECM). Membrane type-1 matrix metalloproteinase (MT1-MMP) facilitates this process and translocates to the plasma membrane following activation to promote ECM cleavage. The N-terminal pro-domain within MT1-MMP must be processed for complete activity of the proteinase. This study investigated whether MT1-MMP activation was altered by sphingosine 1-phosphate (S1P) and wall shear stress (WSS), which combine to stimulate EC invasion in three dimensional (3D) collagen matrices. MT1-MMP was activated rapidly and completely by WSS but not S1P. Proprotein convertases (PCs) promoted MT1-MMP processing, prompting us to test whether WSS or S1P treatments increased PC activity. Like MT1-MMP, PC activity increased with WSS, while S1P had no effect. A pharmacological PC inhibitor completely blocked S1P- and WSS-induced EC invasion and MT1-MMP translocation to the plasma membrane. Further, a recombinant PC inhibitor reduced MT1-MMP activation and decreased lumen formation in invading ECs, a process known to be controlled by MT1-MMP. Thus, we conclude that PC and MT1-MMP activation are mechanosensitive events that are required for EC invasion into 3D collagen matrices.
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Affiliation(s)
- Hojin Kang
- Molecular & Cellular Medicine, Texas A&M Health Science Center, College Station, TX, USA
| | - Camille L Duran
- Molecular & Cellular Medicine, Texas A&M Health Science Center, College Station, TX, USA
| | - Colette A Abbey
- Molecular & Cellular Medicine, Texas A&M Health Science Center, College Station, TX, USA
| | - Roland R Kaunas
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Kayla J Bayless
- Molecular & Cellular Medicine, Texas A&M Health Science Center, College Station, TX, USA.
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Hanna LLH, Sanders JO, Riley DG, Abbey CA, Gill CA. Identification of a major locus interacting with MC1R and modifying black coat color in an F₂ Nellore-Angus population. Genet Sel Evol 2014; 46:4. [PMID: 24460986 PMCID: PMC3924621 DOI: 10.1186/1297-9686-46-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [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: 07/01/2013] [Accepted: 01/08/2014] [Indexed: 01/12/2023] Open
Abstract
Background In cattle, base color is assumed to depend on the enzymatic activity specified by the MC1R locus, i.e. the extension locus, with alleles coding for black (ED), red (e), and wild-type (E+). In most mammals, these alleles are presumed to follow the dominance model of ED > E+ > e, although exceptions are found. In Bos indicus x Bos taurus F2 cattle, some EDE+ heterozygotes are discordant with the dominance series for MC1R and display various degrees of red pigmentation on an otherwise predicted black background. The objective of this study was to identify loci that modify black coat color in these individuals. Results Reddening was classified with a subjective scoring system. Interval analyses identified chromosome-wide suggestive (P < 0.05) and significant (P < 0.01) QTL on bovine chromosomes (BTA) 4 and 5, although these were not confirmed using single-marker association or Bayesian methods. Evidence of a major locus (F = 114.61) that affects reddening was detected between 60 and 73 Mb on BTA 6 (Btau4.0 build), and at 72 Mb by single-marker association and Bayesian methods. The posterior mean of the genetic variance for this region accounted for 43.75% of the genetic variation in reddening. This region coincided with a cluster of tyrosine kinase receptor genes (PDGFRA, KIT and KDR). Fitting SNP haplotypes for a 1 Mb interval that contained all three genes and centered on KIT accounted for the majority of the variation attributed to this major locus, which suggests that one of these genes or associated regulatory elements, is responsible for the majority of variation in degree of reddening. Conclusions Recombinants in a 5 Mb region surrounding the cluster of tyrosine kinase receptor genes implicated PDGFRA as the strongest positional candidate gene. A higher density marker panel and functional analyses will be required to validate the role of PDGFRA or other regulatory variants and their interaction with MC1R for the modification of black coat color in Bos indicus influenced cattle.
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Affiliation(s)
| | | | | | | | - Clare A Gill
- Department of Animal Science, Texas A& M University, College Station, TX 77843, USA.
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Dave JM, Kang H, Abbey CA, Maxwell SA, Bayless KJ. Proteomic profiling of endothelial invasion revealed receptor for activated C kinase 1 (RACK1) complexed with vimentin to regulate focal adhesion kinase (FAK). J Biol Chem 2013; 288:30720-30733. [PMID: 24005669 DOI: 10.1074/jbc.m113.512467] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Angiogenesis is critical for many physiological and pathological processes. To identify molecules relevant to angiogenesis, we performed a proteomic screen comparing invading versus non-invading endothelial cells in three-dimensional collagen matrices. We found up-regulated levels of receptor for activated C kinase 1 (RACK1) and the intermediate filament protein vimentin that correlated with increased endothelial cell invasion. Because both RACK1 and vimentin have been linked to focal adhesion kinase (FAK), we investigated whether this pathway regulated invasion. RACK1 depletion reduced invasion responses, and this was associated with attenuated activation of FAK. Knockdown of vimentin significantly decreased levels of phosphorylated and total FAK. Treatment with a pharmacological inhibitor of FAK dose-dependently reduced invasion, indicating a crucial role for FAK activity during invasion. Because RACK1 and vimentin were both up-regulated with sphingosine 1-phosphate treatment, required for invasion, and regulated FAK, we tested whether they complexed together. RACK1 complexed with vimentin, and growth factors enhanced this interaction. In addition, RACK1, vimentin, and FAK formed an intermolecular complex in invading endothelial cultures in three dimensions in response to stimulation by sphingosine 1-phosphate and growth factors. Moreover, depletion of RACK1 decreased the association of vimentin and FAK, suggesting that RACK1 was required for stabilizing vimentin-FAK interactions during sprouting. Silencing of vimentin and RACK1 decreased cell adhesion and focal contact formation. Taken together, these results demonstrate that proangiogenic signals converge to enhance expression and association of RACK1 and vimentin, which regulated FAK, resulting in successful endothelial sprout formation in three-dimensional collagen matrices.
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Affiliation(s)
- Jui M Dave
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Hojin Kang
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Colette A Abbey
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Steve A Maxwell
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843
| | - Kayla J Bayless
- From the Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, Texas 77843.
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12
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Patterson JL, Abbey CA, Bayless KJ, Bondos SE. Materials composed of the Drosophila melanogaster protein ultrabithorax are cytocompatible. J Biomed Mater Res A 2013; 102:97-104. [PMID: 23596050 DOI: 10.1002/jbm.a.34675] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 02/13/2013] [Accepted: 02/15/2013] [Indexed: 01/01/2023]
Abstract
The Drosophila melanogaster Hox protein ultrabithorax (Ubx) has the interesting ability to hierarchically self-assemble in vitro into materials that have mechanical properties comparable to natural elastin. Ubx materials can be easily functionalized by gene fusion, generating potentially useful scaffolds for cell and tissue engineering. Here, we tested the cytocompatibility of fibers composed of Ubx or an mCherry-Ubx fusion protein. Fibers were cultured with three primary human cell lines derived from vasculature at low passage: umbilical vein endothelial cells, brain vascular pericytes, or aortic smooth muscle cells. No direct or indirect toxicity was observed for any cell line, in response to fibers composed of either plain Ubx or mCherry-Ubx. Cells readily adhered to Ubx fibers, and cells attached to fibers could be transferred between tissue cultures without loss of viability for at least 96 h. When attached to fibers, the morphology of the three cell lines differed somewhat, but all cells in contact with Ubx fibers exhibited a microtubular network aligned with the long axis of Ubx fibers. Thus, Ubx fibers are cytocompatible with cultured primary human vascular cells.
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Affiliation(s)
- Jan L Patterson
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M Health Science Center, College Station, Texas 77843-1114
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13
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Stafuzza NB, Greco AJ, Grant JR, Abbey CA, Gill CA, Raudsepp T, Skow LC, Womack JE, Riggs PK, Amaral MEJ. A high-resolution radiation hybrid map of the river buffalo major histocompatibility complex and comparison with BoLA. Anim Genet 2012; 44:369-76. [PMID: 23216319 DOI: 10.1111/age.12015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2012] [Indexed: 02/03/2023]
Abstract
The major histocompatibility complex (MHC) in mammals codes for antigen-presenting proteins. For this reason, the MHC is of great importance for immune function and animal health. Previous studies revealed this gene-dense and polymorphic region in river buffalo to be on the short arm of chromosome 2, which is homologous to cattle chromosome 23. Using cattle-derived STS markers and a river buffalo radiation hybrid (RH) panel (BBURH5000 ), we generated a high-resolution RH map of the river buffalo MHC region. The buffalo MHC RH map (cR5000 ) was aligned with the cattle MHC RH map (cR12000 ) to compare gene order. The buffalo MHC had similar organization to the cattle MHC, with class II genes distributed in two segments, class IIa and class IIb. Class IIa was closely associated with the class I and class III regions, and class IIb was a separate cluster. A total of 53 markers were distributed into two linkage groups based on a two-point LOD score threshold of ≥8. The first linkage group included 32 markers from class IIa, class I and class III. The second linkage group included 21 markers from class IIb. Bacterial artificial chromosome clones for seven loci were mapped by fluorescence in situ hybridization on metaphase chromosomes using single- and double-color hybridizations. The order of cytogenetically mapped markers in the region corroborated the physical order of markers obtained from the RH map and served as anchor points to align and orient the linkage groups.
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Affiliation(s)
- N B Stafuzza
- Department of Biology, UNESP - São Paulo State University, IBILCE, Sao Jose do Rio Preto, SP, 15054-000, Brazil
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14
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Stafuzza NB, Abbey CA, Gill CA, Womack JE, Amaral MEJ. Construction and preliminary characterization of a river buffalo bacterial artificial chromosome library. Genet Mol Res 2012; 11:3013-9. [PMID: 22653673 DOI: 10.4238/2012.may.22.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
River buffalo genome analyses have advanced significantly in the last decade, and the genome sequence of Bubalus bubalis will be available shortly. Nonetheless, large-insert DNA library resources such as bacterial artificial chromosomes (BAC) are still required for validation and accurate assembly of the genome sequence. We constructed a river buffalo BAC library containing 52,224 clones with an average insert size of 97 kb, representing 1.7 × coverage of the genome. This genomic resource for river buffalo will facilitate further studies in this economically important species allowing for instance, whole genome physical mapping and isolation of genes and gene clusters, contributing to the elucidation of gene organization and identification of regulatory elements.
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Affiliation(s)
- N B Stafuzza
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual de São Paulo "Júlio de Mesquita Filho", São José do Rio Preto, SP, Brazil
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15
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Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigó R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Câmara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FSL, Lau LPL, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CTA, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JGR, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJM, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL, Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo ARR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IKFDM, de Oliveira CJF, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JCM, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, Moré DD, Muntean CT, Nandakumar HP, Nogueira MFG, Olsaker I, Pant SD, Panzitta F, Pastor RCP, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BPVL, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH, White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 2009; 324:522-8. [PMID: 19390049 DOI: 10.1126/science.1169588] [Citation(s) in RCA: 806] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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16
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Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, Gill CA, Green RD, Hamernik DL, Kappes SM, Lien S, Matukumalli LK, McEwan JC, Nazareth LV, Schnabel RD, Weinstock GM, Wheeler DA, Ajmone-Marsan P, Boettcher PJ, Caetano AR, Garcia JF, Hanotte O, Mariani P, Skow LC, Sonstegard TS, Williams JL, Diallo B, Hailemariam L, Martinez ML, Morris CA, Silva LOC, Spelman RJ, Mulatu W, Zhao K, Abbey CA, Agaba M, Araujo FR, Bunch RJ, Burton J, Gorni C, Olivier H, Harrison BE, Luff B, Machado MA, Mwakaya J, Plastow G, Sim W, Smith T, Thomas MB, Valentini A, Williams P, Womack J, Woolliams JA, Liu Y, Qin X, Worley KC, Gao C, Jiang H, Moore SS, Ren Y, Song XZ, Bustamante CD, Hernandez RD, Muzny DM, Patil S, San Lucas A, Fu Q, Kent MP, Vega R, Matukumalli A, McWilliam S, Sclep G, Bryc K, Choi J, Gao H, Grefenstette JJ, Murdoch B, Stella A, Villa-Angulo R, Wright M, Aerts J, Jann O, Negrini R, Goddard ME, Hayes BJ, Bradley DG, Barbosa da Silva M, Lau LPL, Liu GE, Lynn DJ, Panzitta F, Dodds KG. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 2009; 324:528-32. [PMID: 19390050 PMCID: PMC2735092 DOI: 10.1126/science.1167936] [Citation(s) in RCA: 561] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.
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17
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Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Aerts J, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt R, Jann O, Jones SJM, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas FW, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel RD, Silveri L, Skow LC, Smith TPL, Sonstegard TS, Taylor JF, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G, Zhao S. A physical map of the bovine genome. Genome Biol 2008; 8:R165. [PMID: 17697342 PMCID: PMC2374996 DOI: 10.1186/gb-2007-8-8-r165] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 07/20/2007] [Accepted: 08/14/2007] [Indexed: 11/10/2022] Open
Abstract
A new physical map of the bovine genome has been constructed by integrating data from genetic and radiation hybrid maps, and a new bovine BAC map, with the bovine genome draft assembly. Background Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project. Results A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly. Conclusion Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans.
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Affiliation(s)
- Warren M Snelling
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Readman Chiu
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Jacqueline E Schein
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Matthew Hobbs
- Cooperative Research Centre for Innovative Dairy Products, Reprogen, Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | | | | | - Jan Aerts
- Roslin Institute, Roslin, Midlothian EH25 9PS, UK
| | - Gary L Bennett
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Ian E Bosdet
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Mekki Boussaha
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | | | - Alexandre R Caetano
- Embrapa Recursos Geneticos e Biotecnologia, Parque Estacao Biologica, Final Av. W/5 Norte, Brasilia-DF, CP 02372 70770-900, Brasil
| | - Marcos M Costa
- Embrapa Recursos Geneticos e Biotecnologia, Parque Estacao Biologica, Final Av. W/5 Norte, Brasilia-DF, CP 02372 70770-900, Brasil
| | | | - Brian P Dalrymple
- CSIRO Livestock Industries, Carmody Road, St Lucia, Queensland 4067, Australia
| | - André Eggen
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | | | - Sandrine Floriot
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | - Mathieu Gautier
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | - Clare A Gill
- Texas A&M University, College Station, TX 77843, USA
| | - Ronnie D Green
- USDA-ARS - National Program Staff, Beltsville, MD 20705-5134, USA
| | - Robert Holt
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Oliver Jann
- Roslin Institute, Roslin, Midlothian EH25 9PS, UK
| | - Steven JM Jones
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Steven M Kappes
- USDA-ARS - National Program Staff, Beltsville, MD 20705-5134, USA
| | - John W Keele
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Pieter J de Jong
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
| | - Denis M Larkin
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Harris A Lewin
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Stephanie McKay
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Marco A Marra
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Carrie A Mathewson
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Stephen S Moore
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Brenda Murdoch
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Frank W Nicholas
- Cooperative Research Centre for Innovative Dairy Products, Reprogen, Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia
| | - Kazutoyo Osoegawa
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA
| | - Alice Roy
- Genoscope, rue Gaston Cremieux, 91057 Evry, France
| | - Hanni Salih
- Texas A&M University, College Station, TX 77843, USA
| | - Laurent Schibler
- INRA, UR339 Laboratoire de Génétique Biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
| | - Robert D Schnabel
- Animal Science Research Center, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Licia Silveri
- Istituto di Zootecnica Università Cattolica del S Cuore, via E Parmense, 84 29100 Piacenza, Italy
| | - Loren C Skow
- Texas A&M University, College Station, TX 77843, USA
| | - Timothy PL Smith
- USDA, ARS, US Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Tad S Sonstegard
- USDA, ARS, BARC Bovine Functional Genomics Laboratory, Maryland, USA
| | - Jeremy F Taylor
- Animal Science Research Center, Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Ross Tellam
- CSIRO Livestock Industries, Carmody Road, St Lucia, Queensland 4067, Australia
| | | | - John L Williams
- Roslin Institute, Roslin, Midlothian EH25 9PS, UK
- Current address: Parco Tecnologico Padano, Via Einstein, Polo Universitario, Lodi 26900, Italy
| | | | - Natasja H Wye
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - George Yang
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Shaying Zhao
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
- Current address: Department of Biochemistry and Molecular Biology, University of Georgia, Green Street, Athens, GA 30602-7229, USA
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Hansen GR, Abbey CA, Gaile DP, Raudsepp T, Chowdhary BP, Womack JE, Gill CA. Assignment of six genes to bovine chromosomes 5 and 16 by fluorescence in situ hybridization, radiation hybrid mapping and genetic linkage analysis. Cytogenet Genome Res 2007; 116:194-7. [PMID: 17317959 DOI: 10.1159/000098186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Accepted: 11/08/2006] [Indexed: 11/19/2022] Open
Abstract
Several quantitative trait loci for beef carcass traits have been mapped to bovine chromosome 5. The objective of this study was to map six candidate genes for these traits by fluoresence in situ hybridization, genetic linkage analysis and radiation hybrid mapping. MYF5 and MYF6 were assigned to 5q13, WIF1 to 5q23 and MMP19 to 5q25. A paralog of MYF5 (putatively MYOG) was assigned to 16q12. A novel microsatellite placed MYF5 and MYF6 10.4 cM from BM6026 and 19.1 cM from BL23 on the genetic linkage map. MYF5 (62.6 cR), WNT10B (319.5 cR), WIF1 (500.8 cR) and MMP19 (701.2 cR) were also integrated into the 5000(Rad) radiation hybrid map.
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Affiliation(s)
- G R Hansen
- Department of Animal Science, Texas A&M University, College Station, TX, USA.
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19
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Wunderlich KR, Abbey CA, Clayton DR, Song Y, Schein JE, Georges M, Coppieters W, Adelson DL, Taylor JF, Davis SL, Gill CA. A 2.5-Mb contig constructed from Angus, Longhorn and horned Hereford DNA spanning the polled interval on bovine chromosome 1. Anim Genet 2007; 37:592-4. [PMID: 17121607 DOI: 10.1111/j.1365-2052.2006.01538.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [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: 11/29/2022]
Abstract
The polled locus has been mapped by genetic linkage analysis to the proximal region of bovine chromosome 1. As an intermediate step in our efforts to identify the polled locus and the underlying causative mutation for the polled phenotype, we have constructed a BAC-based physical map of the interval containing the polled locus. Clones containing genes and markers in the critical interval were isolated from the TAMBT (constructed from Angus and Longhorn genomic DNA) and CHORI-240 (constructed from horned Hereford genomic DNA) BAC libraries and ordered based on fingerprinting and the presence or absence of 80 STS markers. A single contig spanning 2.5 Mb was assembled. Comparison of the physical order of STSs to the corresponding region of human chromosome 21 revealed the same order of genes within the polled critical interval. This contig of overlapping BAC clones from horned and polled breeds is a useful resource for SNP discovery and characterization of positional candidate genes.
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Affiliation(s)
- K R Wunderlich
- Department of Animal Science, Texas A&M University, College Station, TX 77843, USA
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Gray CA, Abbey CA, Beremand PD, Choi Y, Farmer JL, Adelson DL, Thomas TL, Bazer FW, Spencer TE. Identification of endometrial genes regulated by early pregnancy, progesterone, and interferon tau in the ovine uterus. Biol Reprod 2005; 74:383-94. [PMID: 16251498 DOI: 10.1095/biolreprod.105.046656] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.3] [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] [Indexed: 11/01/2022] Open
Abstract
During early pregnancy in ruminants, progesterone (P4) from the corpus luteum and interferon tau (IFNT) from the conceptus act on the endometrium to regulate genes important for uterine receptivity and conceptus growth. The use of the uterine gland knockout (UGKO) ewe has demonstrated the critical role of epithelial secretions in regulation of conceptus survival and growth. A custom ovine cDNA array was used to identify alterations in gene expression of endometria from Day 14 cyclic, pregnant, and UGKO ewes (study 1) and from cyclic ewes treated with P4 or P4 with ZK 136,317 antiprogestin and control proteins or IFNT (study 2). In study 1, expression of 47 genes was more than 2-fold different between Day 14 pregnant and cyclic endometria, whereas 23 genes was different between Day 14 cyclic and UGKO endometria. In study 2, 70 genes were different due to P4 alone, 74 genes were affected by IFNT in a P4-dependent manner, and 180 genes were regulated by IFNT in a P4-independent manner. In each study, an approximately equal number of genes were found to be activated or repressed in each group. Endometrial genes increased by pregnancy and P4 and/or IFNT include B2M, CTSL, CXCL10, G1P3, GRP, IFI27, IFIT1, IFITM3, LGALS15, MX1, POSTN, RSAD2, and STAT5A. Transcripts decreased by pregnancy and P4 and/or IFNT include COL3A1, LUM, PTMA, PUM1, RPL9, SPARC, and VIM. Identification and analysis of these hormonally responsive genes will help define endometrial pathways critical for uterine support of peri-implantation conceptus survival, growth, and implantation.
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Affiliation(s)
- C Allison Gray
- Center for Animal Biotechnology and Genomics, Texas A&M University, College Station, Texas 77843, USA
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Ward TL, Valberg SJ, Adelson DL, Abbey CA, Binns MM, Mickelson JR. Glycogen branching enzyme (GBE1) mutation causing equine glycogen storage disease IV. Mamm Genome 2004; 15:570-7. [PMID: 15366377 DOI: 10.1007/s00335-004-2369-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [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: 10/26/2022]
Abstract
Comparative biochemical and histopathological evidence suggests that a deficiency in the glycogen branching enzyme, encoded by the GBE1 gene, is responsible for a recently identified recessive fatal fetal and neonatal glycogen storage disease (GSD) in American Quarter Horses termed GSD IV. We have now derived the complete GBE1 cDNA sequences for control horses and affected foals, and identified a C to A substitution at base 102 that results in a tyrosine (Y) to stop (X) mutation in codon 34 of exon 1. All 11 affected foals were homozygous for the X34 allele, their 11 available dams and sires were heterozygous, and all 16 control horses were homozygous for the Y34 allele. The previous findings of poorly branched glycogen, abnormal polysaccharide accumulation, lack of measurable GBE1 enzyme activity and immunodetectable GBE1 protein, coupled with the present observation of abundant GBE1 mRNA in affected foals, are all consistent with the nonsense mutation in the 699 amino acid GBE1 protein. The affected foal pedigrees have a common ancestor and contain prolific stallions that are likely carriers of the recessive X34 allele. Defining the molecular basis of equine GSD IV will allow for accurate DNA testing and the ability to prevent occurrence of this devastating disease affecting American Quarter Horses and related breeds.
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Affiliation(s)
- Tara L Ward
- Department of Veterinary PathoBiology, College of Veterinary Medicine, University of Minnesota, 295 AS/VM, 1988 Fitch Ave., St. Paul, Minnesota 55108-6009, USA
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White SN, Taylor KH, Abbey CA, Gill CA, Womack JE. Haplotype variation in bovine Toll-like receptor 4 and computational prediction of a positively selected ligand-binding domain. Proc Natl Acad Sci U S A 2003; 100:10364-9. [PMID: 12915733 PMCID: PMC193567 DOI: 10.1073/pnas.1333957100] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [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: 11/18/2022] Open
Abstract
Toll-like receptor 4 (TLR4) is a cell-surface receptor that activates innate and adaptive immune responses. Because it recognizes a broad class of pathogen-associated molecular patterns presented by lipopolysaccharides and lipoteichoic acid, TLR4 is a candidate gene for resistance to a large number of diseases. In particular, mouse models suggest TLR4 as a candidate gene for resistance to major agents in bovine respiratory disease and Johne's disease. The coding sequence of bovine TLR4 is divided into three exons, with intron/exon boundaries and intron sizes similar to those of human TLR4 transcript variant 1. We amplified each exon in 40 individuals from 11 breeds and screened the sequence for single-nucleotide polymorphisms (SNPs). We identified 32 SNPs, 28 of which are in the coding sequence, for an average of one SNP per 90 bp of coding sequence. Eight SNPs were nonsynonymous and potentially alter specificity of pathogen recognition or efficiency of signaling. To evaluate the functional importance of these SNPs, we used codon-substitution models to detect diversifying selection in an extracellular region that may physically interact with ligands. One nonsynonymous SNP is located within this region, and other substitutions are in adjacent regions that may interact with coreceptor molecules. The 32 SNPs were found in 20 haplotypes that can be assigned to geographic ranges of origin. Haplotype-tagging SNP analysis indicated that 12 SNPs need to be genotyped to distinguish these 20 haplotypes. These data provide a basic understanding of bovine TLR4 sequence variation and supply haplotype markers for disease association studies.
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Affiliation(s)
- Stephen N White
- Department of Veterinary Pathobiology and Animal Science, Texas A&M University, College Station, TX 77843, USA
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O'Malley KG, Abbey CA, Ross K, Gold JR. Microsatellite DNA markers for kinship analysis and genetic mapping in red drum, Sciaenops ocellatus (Sciaenidae, Teleostei). ACTA ACUST UNITED AC 2003. [DOI: 10.1046/j.1471-8286.2003.00379.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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