Thrombospondin-1 Promotes Matrix Homeostasis by Interacting with Collagen and Lysyl Oxidase Precursors and Collagen Cross-Linking Sites
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Methylome and Transcriptome Maps of Human Visceral and Subcutaneous
www.nature.com/scientificreports OPEN Methylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal Received: 9 April 2019 Accepted: 11 June 2019 key epigenetic diferences at Published: xx xx xxxx developmental genes Stephen T. Bradford1,2,3, Shalima S. Nair1,3, Aaron L. Statham1, Susan J. van Dijk2, Timothy J. Peters 1,3,4, Firoz Anwar 2, Hugh J. French 1, Julius Z. H. von Martels1, Brodie Sutclife2, Madhavi P. Maddugoda1, Michelle Peranec1, Hilal Varinli1,2,5, Rosanna Arnoldy1, Michael Buckley1,4, Jason P. Ross2, Elena Zotenko1,3, Jenny Z. Song1, Clare Stirzaker1,3, Denis C. Bauer2, Wenjia Qu1, Michael M. Swarbrick6, Helen L. Lutgers1,7, Reginald V. Lord8, Katherine Samaras9,10, Peter L. Molloy 2 & Susan J. Clark 1,3 Adipocytes support key metabolic and endocrine functions of adipose tissue. Lipid is stored in two major classes of depots, namely visceral adipose (VA) and subcutaneous adipose (SA) depots. Increased visceral adiposity is associated with adverse health outcomes, whereas the impact of SA tissue is relatively metabolically benign. The precise molecular features associated with the functional diferences between the adipose depots are still not well understood. Here, we characterised transcriptomes and methylomes of isolated adipocytes from matched SA and VA tissues of individuals with normal BMI to identify epigenetic diferences and their contribution to cell type and depot-specifc function. We found that DNA methylomes were notably distinct between diferent adipocyte depots and were associated with diferential gene expression within pathways fundamental to adipocyte function. Most striking diferential methylation was found at transcription factor and developmental genes. Our fndings highlight the importance of developmental origins in the function of diferent fat depots. -
140503 IPF Signatures Supplement Withfigs Thorax
Supplementary material for Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis Daryle J. DePianto1*, Sanjay Chandriani1⌘*, Alexander R. Abbas1, Guiquan Jia1, Elsa N. N’Diaye1, Patrick Caplazi1, Steven E. Kauder1, Sabyasachi Biswas1, Satyajit K. Karnik1#, Connie Ha1, Zora Modrusan1, Michael A. Matthay2, Jasleen Kukreja3, Harold R. Collard2, Jackson G. Egen1, Paul J. Wolters2§, and Joseph R. Arron1§ 1Genentech Research and Early Development, South San Francisco, CA 2Department of Medicine, University of California, San Francisco, CA 3Department of Surgery, University of California, San Francisco, CA ⌘Current address: Novartis Institutes for Biomedical Research, Emeryville, CA. #Current address: Gilead Sciences, Foster City, CA. *DJD and SC contributed equally to this manuscript §PJW and JRA co-directed this project Address correspondence to Paul J. Wolters, MD University of California, San Francisco Department of Medicine Box 0111 San Francisco, CA 94143-0111 [email protected] or Joseph R. Arron, MD, PhD Genentech, Inc. MS 231C 1 DNA Way South San Francisco, CA 94080 [email protected] 1 METHODS Human lung tissue samples Tissues were obtained at UCSF from clinical samples from IPF patients at the time of biopsy or lung transplantation. All patients were seen at UCSF and the diagnosis of IPF was established through multidisciplinary review of clinical, radiological, and pathological data according to criteria established by the consensus classification of the American Thoracic Society (ATS) and European Respiratory Society (ERS), Japanese Respiratory Society (JRS), and the Latin American Thoracic Association (ALAT) (ref. 5 in main text). Non-diseased normal lung tissues were procured from lungs not used by the Northern California Transplant Donor Network. -
Time-Series Plasma Cell-Free DNA Analysis Reveals Disease Severity of COVID-19 Patients
medRxiv preprint doi: https://doi.org/10.1101/2020.06.08.20124305; this version posted June 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Time-series plasma cell-free DNA analysis reveals disease severity of COVID- 19 patients Authors: Xinping Chen1†, Yu Lin2†, Tao Wu1†, Jinjin Xu2†, Zhichao Ma1†, Kun Sun2,5†, Hui Li1†, Yuxue Luo2,3†, Chen Zhang1, Fang Chen2, Jiao Wang1, Tingyu Kuo2,4, Xiaojuan Li1, Chunyu Geng2, Feng Lin1, Chaojie Huang2, Junjie Hu1, Jianhua Yin2, Ming Liu1, Ye Tao2, Jiye Zhang1, Rijing Ou2, Furong Xiao1, Huanming Yang2,6, Jian Wang2,6, Xun Xu2,7, Shengmiao Fu1*, Xin Jin2,3*, Hongyan Jiang1*, Ruoyan Chen2* Affiliations: 1Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational Medicine, Haikou 570311, Hainan, China. 2BGI-Shenzhen, Shenzhen, 518083, Guangdong, China 3School of Medicine, South China University of Technology, Guangzhou 510006, Guangdong, China 4BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, China 5Shenzhen Bay Laboratory, Shenzhen 518132, Guangdong, China 6James D. Watson Institute of Genome Sciences, Hangzhou 310058, China 7Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China *Correspondence to: [email protected]; [email protected]; [email protected]; [email protected]. †These authors contributed equally to this work. Abstract: Clinical symptoms of coronavirus disease 2019 (COVID-19) range from asymptomatic to severe pneumonia and death. -
Gingival!Health!Transcriptome!
! ! ! Gingival!Health!Transcriptome! ! Thesis! ! Presented!in!Partial!Fulfillment!of!the!Requirements!for!the!Degree!Master!of! Science!in!the!Graduate!School!of!The!Ohio!State!University! ! By! Christina!Zachariadou,!DDS! Graduate!Program!in!Dentistry! The!Ohio!State!University! 2018! ! ! Thesis!Committee:! Angelo!J.!Mariotti,!DDS,!PhD,!Advisor! Thomas!C.!Hart,!DDS,!PhD! John!D.!Walters,!DDS,!MMSc! ! ! ! 1! ! ! ! ! ! ! ! ! ! ! Copyright!by! Christina!Zachariadou! 2018! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! 2! ! ! ! Abstract! ! Introduction:!In!the!field!of!periodontology,!a!satisfactory!definition!of!periodontal! health!is!lacking.!Instead,!clinicians!use!surrogate!measures,!such!as!color,!texture,! consistency,!probing!depths!and!bleeding!on!probing!to!examine!periodontal!tissues! and! diagnose! disease,! or! the! absence! of! it,! which! they! define! as! “clinical! health”.!! Additionally,!it!has!been!shown!that!age!progression!is!accompanied!by!changes!in! the!periodontium.!As!a!result,!understanding!the!gene!expression!in!healthy!gingiva,! through!the!field!of!transcriptomics,!could!provide!some!insight!on!the!molecules! that!contribute!to!gingival!health.!Also,!comparing!the!transcriptome!of!young!and! older!subjects,!taking!into!consideration!the!effect!of!sex/gender,!can!shed!light!on! differential! gene! expression! with! age! progression! and! on! individual! differences! between! sexes,! and! may! provide! future! therapeutic! endpoints! of! periodontal! treatment.!The!main!focus!of!this!study!was!to!ascertain!collagen!(COL)!and!matrix! -
Collagens, Modifying Enzymes and Their Mutations in Humans, Flies And
Review TRENDS in Genetics Vol.20 No.1 January 2004 33 Collagens, modifying enzymes and their mutations in humans, flies and worms Johanna Myllyharju and Kari I. Kivirikko Collagen Research Unit, Biocenter Oulu and Department of Medical Biochemistry and Molecular Biology, University of Oulu, FIN-90014 Oulu, Finland Collagens and proteins with collagen-like domains form Collagens are the most abundant proteins in the human large superfamilies in various species, and the numbers body, constituting ,30% of its protein mass. The import- of known family members are increasing constantly. ant roles of these proteins have been clearly demonstrated Vertebrates have at least 27 collagen types with 42 dis- by the wide spectrum of diseases caused by a large number tinct polypeptide chains, >20 additional proteins with of mutations found in collagen genes. This article will collagen-like domains and ,20 isoenzymes of various review the collagen superfamilies and their mutations in collagen-modifying enzymes. Caenorhabditis elegans vertebrates, Drosophila melanogaster and the nematode has ,175 cuticle collagen polypeptides and two base- Caenorhabditis elegans. The genomes of these two model ment membrane collagens. Drosophila melanogaster invertebrate species have been fully sequenced, and it is has far fewer collagens than many other species but therefore possible to identify all of the collagen genes has ,20 polypeptides similar to the catalytic subunits present in these species. Because of the extensive of prolyl 4-hydroxylase, the key enzyme of collagen syn- literature in these fields, this review will focus primarily thesis. More than 1300 mutations have so far been on recent advances. More detailed accounts and more characterized in 23 of the 42 human collagen genes complete references can be found in previous reviews, for in various diseases, and many mouse models and example Refs [1–6]. -
Single Nucleus RNA-Sequencing Defines Unexpected Diversity Of
ARTICLE https://doi.org/10.1038/s41467-021-22691-2 OPEN Single nucleus RNA-sequencing defines unexpected diversity of cholinergic neuron types in the adult mouse spinal cord Mor R. Alkaslasi 1,2,3, Zoe E. Piccus1,2,3, Sangeetha Hareendran1, Hanna Silberberg1, Li Chen1, Yajun Zhang1, ✉ Timothy J. Petros 1 & Claire E. Le Pichon 1 1234567890():,; In vertebrates, motor control relies on cholinergic neurons in the spinal cord that have been extensively studied over the past hundred years, yet the full heterogeneity of these neurons and their different functional roles in the adult remain to be defined. Here, we develop a targeted single nuclear RNA sequencing approach and use it to identify an array of choli- nergic interneurons, visceral and skeletal motor neurons. Our data expose markers for dis- tinguishing these classes of cholinergic neurons and their rich diversity. Specifically, visceral motor neurons, which provide autonomic control, can be divided into more than a dozen transcriptomic classes with anatomically restricted localization along the spinal cord. The complexity of the skeletal motor neurons is also reflected in our analysis with alpha, gamma, and a third subtype, possibly corresponding to the elusive beta motor neurons, clearly dis- tinguished. In combination, our data provide a comprehensive transcriptomic description of this important population of neurons that control many aspects of physiology and movement and encompass the cellular substrates for debilitating degenerative disorders. 1 Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA. 2 Department of ✉ Neuroscience, Brown University, Providence, RI, USA. 3These authors contributed equally: Mor R. -
Collagen 24 Α1 Is Increased in Insulin-Resistant Skeletal Muscle and Adipose Tissue
International Journal of Molecular Sciences Article Collagen 24 α1 Is Increased in Insulin-Resistant Skeletal Muscle and Adipose Tissue Xiong Weng 1, De Lin 2, Jeffrey T. J. Huang 1, Roland H. Stimson 3 , David H. Wasserman 4 and Li Kang 1,* 1 Division of Systems Medicine, School of Medicine, University of Dundee, Dundee, Scotland DD1 9SY, UK; [email protected] (X.W.); [email protected] (J.T.J.H.) 2 Drug Discovery Unit, University of Dundee, Dundee, Scotland DD1 9SY, UK; [email protected] 3 Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, Scotland EH16 4TJ, UK; [email protected] 4 Department of Molecular Physiology and Biophysics and Mouse Metabolic Phenotyping Centre, Vanderbilt University, Nashville, TN 37232, USA; [email protected] * Correspondence: [email protected]; Tel.: +44-(0)1382-383019 Received: 29 June 2020; Accepted: 2 August 2020; Published: 10 August 2020 Abstract: Aberrant extracellular matrix (ECM) remodelling in muscle, liver and adipose tissue is a key characteristic of obesity and insulin resistance. Despite its emerging importance, the effective ECM targets remain largely undefined due to limitations of current approaches. Here, we developed a novel ECM-specific mass spectrometry-based proteomics technique to characterise the global view of the ECM changes in the skeletal muscle and liver of mice after high fat (HF) diet feeding. We identified distinct signatures of HF-induced protein changes between skeletal muscle and liver where the ECM remodelling was more prominent in the muscle than liver. In particular, most muscle collagen isoforms were increased by HF diet feeding whereas the liver collagens were differentially but moderately affected highlighting a different role of the ECM remodelling in different tissues of obesity. -
And CD45+ Stromal Populations in Extra-Skeletal Tumors With
RESEARCH ARTICLE Osterix-Cre marks distinct subsets of CD45- and CD45+ stromal populations in extra-skeletal tumors with pro- tumorigenic characteristics Biancamaria Ricci1, Eric Tycksen2, Hamza Celik3, Jad I Belle3, Francesca Fontana3, Roberto Civitelli4, Roberta Faccio1,5* 1Department of Orthopedics, Washington University School of Medicine, St. Louis, United States; 2Genome Technology Access Center, Department of Genetics, Washington University School of Medicine, St. Louis, United States; 3Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, United States; 4Department of Medicine, Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, United States; 5Shriners Children Hospital, St. Louis, United States Abstract Cancer-associated fibroblasts (CAFs) are a heterogeneous population of mesenchymal cells supporting tumor progression, whose origin remains to be fully elucidated. Osterix (Osx) is a marker of osteogenic differentiation, expressed in skeletal progenitor stem cells and bone-forming osteoblasts. We report Osx expression in CAFs and by using Osx-cre;TdTomato reporter mice we confirm the presence and pro-tumorigenic function of TdTOSX+ cells in extra-skeletal tumors. Surprisingly, only a minority of TdTOSX+ cells expresses fibroblast and osteogenic markers. The majority of TdTOSX+ cells express the hematopoietic marker CD45, have a genetic and phenotypic profile resembling that of tumor infiltrating myeloid and lymphoid populations, but with higher expression of lymphocytic immune suppressive genes. We find Osx transcript and Osx protein expression early during hematopoiesis, in subsets of hematopoietic stem cells and multipotent *For correspondence: progenitor populations. Our results indicate that Osx marks distinct tumor promoting CD45- and [email protected] CD45+ populations and challenge the dogma that Osx is expressed exclusively in cells of Competing interests: The mesenchymal origin. -
Supplemental Table 1. Qrt-PCR Conditions
Supplemental Table 1. qRT-PCR conditions. Official gene Official Accession Tm Sequence Forward (5’ to 3’) Sequence Reverse (5’ to 3’) symbol gene name number (°C) Neuromedin U NMUR1 NM_006056 60 CAGCCAGGTCCAGATACAC AGCCCAGGTAGAAGAAGATG receptor 1 Actin gamma 2 ACTG2 smooth muscle NM_001615 60 GCTGTCTTCCCCTCCATTG CATTGTAGAAGGAGTGGTGC enteric Short stature SHOX2 NM_003030 60 AGGAGGTGTAGGAGGAGGA GCCTCTGCTTGATTTTGGTC homeobox 2 Bradykinin receptor BDKRB2 NM_000623 58 CCCTGGAAGATATCAATGTTT ACTCCACTTGGGGGCATTT B2 Homeodomain-only HOPX NM_139211 60 GGTGGAAATCCTGGAGTACA GACGGATCTGCACTCTGAG protein homeobox MSX1 Msh homeobox 1 NM_002448 60 TCCTCAAGCTGCCAGAAGAT CTTGTGTTTGCGGAGGGTG Calcium voltage- CACNA1G gated channel NM_018896 58 CCCTTTATTTCATTGCCCTC ATTCGGACTTGTTGGCATCT subunit alpha1 G Actin alpha 2 ACTA2 NM_001613 58 AATGGGACAAAAAGACAGCTA GGGCAACACGAAGCTCATT smooth muscle aorta MYL4 Myosin light chain 4 NM_001002841 58 AAGAAGCCTGAGCCTAAGAA TCTTCATCTCTCCAGTCGG Solute carrier family SLC8A1 NM_021097 58 TTCAAGAGTACTGTGGACAAA ATTCATCGTCGTCATCATCTT 8 member A1 Myosin heavy chain MYH10 NM_001256012 58 AAGCAATGGTCAACAAAGATG ACACAGAAGAGTCCAGAATAA 10 non-muscle Aldehyde ALDH1A2 dehydrogenase 1 NM_003888 58 TTTTTATGTGGATTTGCAGGG AAACATCAGCAGGGGGAAG family member A2 Cholinergic receptor CHRNE nicotinic epsilon NM_000080 58 GTCTTTATCACCATCTCTTCA TGTAGTTGAGTCGGTAATCC subunit 5-hydroxytryptamine HTR2B NM_000867 58 GTTGGATTGTTTGTGATGCC TGGATGCGGTTGAAAAGAGA receptor 2B Potassium/sodium hyperpolarization- HCN2 activated cyclic NM_001194 58 ACTAAGGGCAACAAGGAGAT -
Gene Modules Associated with Human Diseases Revealed By
bioRxiv preprint doi: https://doi.org/10.1101/598151; this version posted April 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Gene modules associated with human diseases revealed by network analysis Shisong Ma1,2, *, Jiazhen Gong1, §, Wanzhu Zuo1, §, Haiying Geng1, Yu Zhang1, Meng Wang1, Ershang Han1, Jing Peng1, Yuzhou Wang1, Yifan Wang1, Yanyan Chen1 1. Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China 2. School of Data Science, University of Science and Technology of China, Hefei, Anhui 230027, China * Corresponding author: Shisong Ma ([email protected]) § These authors contribute equally. bioRxiv preprint doi: https://doi.org/10.1101/598151; this version posted April 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Abstract Within biological networks, genes associated with human diseases likely map to modules whose identification facilitates etiology studies but remains challenging. We describe a systematic approach to identify such disease-associated gene modules. A gene co-expression network was constructed using GTEx dataset and assembled into 652 gene modules. Screening these modules identified those with disease genes enrichment for obesity, cardiomyopathy, hypertension, and autism, which revealed the pathways involved in their pathogenesis. -
Transcriptomic Profiling of Adipose Derived Stem Cells Undergoing
www.nature.com/scientificreports OPEN Transcriptomic Profling of Adipose Derived Stem Cells Undergoing Osteogenesis by RNA-Seq Received: 11 January 2019 Shahensha Shaik1, Elizabeth C. Martin2, Daniel J. Hayes3, Jefrey M. Gimble4 & Accepted: 25 July 2019 Ram V. Devireddy1 Published: xx xx xxxx Adipose-derived stromal/stem cells (ASCs) are multipotent in nature that can be diferentiated into various cells lineages such as adipogenic, osteogenic, and chondrogenic. The commitment of a cell to diferentiate into a particular lineage is regulated by the interplay between various intracellular pathways and their resultant secretome. Similarly, the interactions of cells with the extracellular matrix (ECM) and the ECM bound growth factors instigate several signal transducing events that ultimately determine ASC diferentiation. In this study, RNA-sequencing (RNA-Seq) was performed to identify the transcriptome profle of osteogenic induced ASCs to understand the associated genotype changes. Gene ontology (GO) functional annotations analysis using Database for Annotation Visualization and Integrated Discovery (DAVID) bioinformatics resources on the diferentially expressed genes demonstrated the enrichment of pathways mainly associated with ECM organization and angiogenesis. We, therefore, studied the expression of genes coding for matrisome proteins (glycoproteins, collagens, proteoglycans, ECM-afliated, regulators, and secreted factors) and ECM remodeling enzymes (MMPs, integrins, ADAMTSs) and the expression of angiogenic markers during the osteogenesis of ASCs. The upregulation of several pro-angiogenic ELR+ chemokines and other angiogenic inducers during osteogenesis indicates the potential role of the secretome from diferentiating ASCs in the vascular development and its integration with the bone tissue. Furthermore, the increased expression of regulatory genes such as CTNNB1, TGBR2, JUN, FOS, GLI3, and MAPK3 involved in the WNT, TGF- β, JNK, HedgeHog and ERK1/2 pathways suggests the regulation of osteogenesis through interplay between these pathways. -
Gene Modules Associated with Human Diseases Revealed by Network
bioRxiv preprint doi: https://doi.org/10.1101/598151; this version posted June 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Gene modules associated with human diseases revealed by network analysis Shisong Ma1,2*, Jiazhen Gong1†, Wanzhu Zuo1†, Haiying Geng1, Yu Zhang1, Meng Wang1, Ershang Han1, Jing Peng1, Yuzhou Wang1, Yifan Wang1, Yanyan Chen1 1. Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China 2. School of Data Science, University of Science and Technology of China, Hefei, Anhui 230027, China * To whom correspondence should be addressed. Email: [email protected] † These authors contribute equally. 1 bioRxiv preprint doi: https://doi.org/10.1101/598151; this version posted June 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. ABSTRACT Despite many genes associated with human diseases have been identified, disease mechanisms often remain elusive due to the lack of understanding how disease genes are connected functionally at pathways level. Within biological networks, disease genes likely map to modules whose identification facilitates etiology studies but remains challenging. We describe a systematic approach to identify disease-associated gene modules.