A Grhl2-Dependent Gene Network Controls Trophoblast Branching Morphogenesis
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3 Embryology and Development
BIOL 6505 − INTRODUCTION TO FETAL MEDICINE 3. EMBRYOLOGY AND DEVELOPMENT Arlet G. Kurkchubasche, M.D. INTRODUCTION Embryology – the field of study that pertains to the developing organism/human Basic embryology –usually taught in the chronologic sequence of events. These events are the basis for understanding the congenital anomalies that we encounter in the fetus, and help explain the relationships to other organ system concerns. Below is a synopsis of some of the critical steps in embryogenesis from the anatomic rather than molecular basis. These concepts will be more intuitive and evident in conjunction with diagrams and animated sequences. This text is a synopsis of material provided in Langman’s Medical Embryology, 9th ed. First week – ovulation to fertilization to implantation Fertilization restores 1) the diploid number of chromosomes, 2) determines the chromosomal sex and 3) initiates cleavage. Cleavage of the fertilized ovum results in mitotic divisions generating blastomeres that form a 16-cell morula. The dense morula develops a central cavity and now forms the blastocyst, which restructures into 2 components. The inner cell mass forms the embryoblast and outer cell mass the trophoblast. Consequences for fetal management: Variances in cleavage, i.e. splitting of the zygote at various stages/locations - leads to monozygotic twinning with various relationships of the fetal membranes. Cleavage at later weeks will lead to conjoined twinning. Second week: the week of twos – marked by bilaminar germ disc formation. Commences with blastocyst partially embedded in endometrial stroma Trophoblast forms – 1) cytotrophoblast – mitotic cells that coalesce to form 2) syncytiotrophoblast – erodes into maternal tissues, forms lacunae which are critical to development of the uteroplacental circulation. -
Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis. -
Anti-Rab11 Antibody (ARG41900)
Product datasheet [email protected] ARG41900 Package: 100 μg anti-Rab11 antibody Store at: -20°C Summary Product Description Goat Polyclonal antibody recognizes Rab11 Tested Reactivity Hu, Ms, Rat, Dog, Mk Tested Application IHC-Fr, IHC-P, WB Host Goat Clonality Polyclonal Isotype IgG Target Name Rab11 Antigen Species Mouse Immunogen Purified recombinant peptides within aa. 110 to the C-terminus of Mouse Rab11a, Rab11b and Rab11c (Rab25). Conjugation Un-conjugated Alternate Names RAB11A: Rab-11; Ras-related protein Rab-11A; YL8 RAB11B: GTP-binding protein YPT3; H-YPT3; Ras-related protein Rab-11B RAB25: RAB11C; CATX-8; Ras-related protein Rab-25 Application Instructions Application table Application Dilution IHC-Fr 1:100 - 1:400 IHC-P 1:100 - 1:400 WB 1:250 - 1:2000 Application Note IHC-P: Antigen Retrieval: Heat mediation was recommended. * The dilutions indicate recommended starting dilutions and the optimal dilutions or concentrations should be determined by the scientist. Positive Control Hepa cell lysate Calculated Mw 24 kDa Observed Size ~ 26 kDa Properties Form Liquid Purification Affinity purification with immunogen. Buffer PBS, 0.05% Sodium azide and 20% Glycerol. Preservative 0.05% Sodium azide www.arigobio.com 1/3 Stabilizer 20% Glycerol Concentration 3 mg/ml Storage instruction For continuous use, store undiluted antibody at 2-8°C for up to a week. For long-term storage, aliquot and store at -20°C. Storage in frost free freezers is not recommended. Avoid repeated freeze/thaw cycles. Suggest spin the vial prior to opening. The antibody solution should be gently mixed before use. Note For laboratory research only, not for drug, diagnostic or other use. -
PARSANA-DISSERTATION-2020.Pdf
DECIPHERING TRANSCRIPTIONAL PATTERNS OF GENE REGULATION: A COMPUTATIONAL APPROACH by Princy Parsana A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2020 © 2020 Princy Parsana All rights reserved Abstract With rapid advancements in sequencing technology, we now have the ability to sequence the entire human genome, and to quantify expression of tens of thousands of genes from hundreds of individuals. This provides an extraordinary opportunity to learn phenotype relevant genomic patterns that can improve our understanding of molecular and cellular processes underlying a trait. The high dimensional nature of genomic data presents a range of computational and statistical challenges. This dissertation presents a compilation of projects that were driven by the motivation to efficiently capture gene regulatory patterns in the human transcriptome, while addressing statistical and computational challenges that accompany this data. We attempt to address two major difficulties in this domain: a) artifacts and noise in transcriptomic data, andb) limited statistical power. First, we present our work on investigating the effect of artifactual variation in gene expression data and its impact on trans-eQTL discovery. Here we performed an in-depth analysis of diverse pre-recorded covariates and latent confounders to understand their contribution to heterogeneity in gene expression measurements. Next, we discovered 673 trans-eQTLs across 16 human tissues using v6 data from the Genotype Tissue Expression (GTEx) project. Finally, we characterized two trait-associated trans-eQTLs; one in Skeletal Muscle and another in Thyroid. Second, we present a principal component based residualization method to correct gene expression measurements prior to reconstruction of co-expression networks. -
Human Germ/Stem Cell-Specific Gene TEX19 Influences Cancer Cell
Planells-Palop et al. Molecular Cancer (2017) 16:84 DOI 10.1186/s12943-017-0653-4 RESEARCH Open Access Human germ/stem cell-specific gene TEX19 influences cancer cell proliferation and cancer prognosis Vicente Planells-Palop1, Ali Hazazi1, Julia Feichtinger2,3, Jana Jezkova1, Gerhard Thallinger2,3, Naif O. Alsiwiehri1, Mikhlid Almutairi1,5, Lee Parry4, Jane A. Wakeman1 and Ramsay J. McFarlane1* Abstract Background: Cancer/testis (CT) genes have expression normally restricted to the testis, but become activated during oncogenesis, so they have excellent potential as cancer-specific biomarkers. Evidence is starting to emerge to indicate that they also provide function(s) in the oncogenic programme. Human TEX19 is a recently identified CT gene, but a functional role for TEX19 in cancer has not yet been defined. Methods: siRNA was used to deplete TEX19 levels in various cancer cell lines. This was extended using shRNA to deplete TEX19 in vivo. Western blotting, fluorescence activated cell sorting and immunofluorescence were used to study the effect of TEX19 depletion in cancer cells and to localize TEX19 in normal testis and cancer cells/tissues. RT-qPCR and RNA sequencing were employed to determine the changes to the transcriptome of cancer cells depleted for TEX19 and Kaplan-Meier plots were generated to explore the relationship between TEX19 expression and prognosis for a range of cancer types. Results: Depletion of TEX19 levels in a range of cancer cell lines in vitro and in vivo restricts cellular proliferation/ self-renewal/reduces tumour volume, indicating TEX19 is required for cancer cell proliferative/self-renewal potential. Analysis of cells depleted for TEX19 indicates they enter a quiescent-like state and have subtle defects in S-phase progression. -
Neonate Germinal Stage Blastocyst Embryonic Disk Trophoblast Umbilical Cord Placenta Embryonic Stage Cephalocaudal Proximodistal
neonate umbilical cord Chapter 3 Chapter 3 germinal stage placenta Chapter 3 Chapter 3 blastocyst embryonic stage Chapter 3 Chapter 3 embryonic disk cephalocaudal Chapter 3 Chapter 3 trophoblast proximodistal Chapter 3 Chapter 3 A tube that connects the fetus to the placenta. A newborn baby. Chapter 3 Chapter 3 An organ connected to the uterine wall and to the fetus by the umbilical cord. The placenta The period of development between conception serves as a filter between mother and fetus for and the implantation of the embryo. the exchange of nutrients and wastes. Chapter 3 Chapter 3 The stage of prenatal development that lasts A stage within the germinal period of prenatal from implantation through the eighth week of development in which the zygote has the form pregnancy; it is characterized by the of a sphere of cells surrounding a cavity of fluid. development of the major organ systems. Chapter 3 Chapter 3 The platelike inner part of the blastocyst that From head to tail. differentiates into the ectoderm, mesoderm, and endoderm of the embryo. Chapter 3 Chapter 3 The outer part of the blastocyst from which the From the inner part (or axis) of the body amniotic sac, placenta, and umbilical cord outward. develop. Chapter 3 Chapter 3 ectoderm amniotic sac Chapter 3 Chapter 3 neural tube amniotic fluid Chapter 3 Chapter 3 endoderm fetal stage Chapter 3 Chapter 3 mesoderm stillbirth Chapter 3 Chapter 3 androgens teratogens Chapter 3 Chapter 3 The outermost cell layer of the newly formed The sac containing the fetus. embryo from which the skin and nervous system develop. -
Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2
Supplementary Table 3 Complete list of RNA-Sequencing analysis of gene expression changed by ≥ tenfold between xenograft and cells cultured in 10%O2 Expr Log2 Ratio Symbol Entrez Gene Name (culture/xenograft) -7.182 PGM5 phosphoglucomutase 5 -6.883 GPBAR1 G protein-coupled bile acid receptor 1 -6.683 CPVL carboxypeptidase, vitellogenic like -6.398 MTMR9LP myotubularin related protein 9-like, pseudogene -6.131 SCN7A sodium voltage-gated channel alpha subunit 7 -6.115 POPDC2 popeye domain containing 2 -6.014 LGI1 leucine rich glioma inactivated 1 -5.86 SCN1A sodium voltage-gated channel alpha subunit 1 -5.713 C6 complement C6 -5.365 ANGPTL1 angiopoietin like 1 -5.327 TNN tenascin N -5.228 DHRS2 dehydrogenase/reductase 2 leucine rich repeat and fibronectin type III domain -5.115 LRFN2 containing 2 -5.076 FOXO6 forkhead box O6 -5.035 ETNPPL ethanolamine-phosphate phospho-lyase -4.993 MYO15A myosin XVA -4.972 IGF1 insulin like growth factor 1 -4.956 DLG2 discs large MAGUK scaffold protein 2 -4.86 SCML4 sex comb on midleg like 4 (Drosophila) Src homology 2 domain containing transforming -4.816 SHD protein D -4.764 PLP1 proteolipid protein 1 -4.764 TSPAN32 tetraspanin 32 -4.713 N4BP3 NEDD4 binding protein 3 -4.705 MYOC myocilin -4.646 CLEC3B C-type lectin domain family 3 member B -4.646 C7 complement C7 -4.62 TGM2 transglutaminase 2 -4.562 COL9A1 collagen type IX alpha 1 chain -4.55 SOSTDC1 sclerostin domain containing 1 -4.55 OGN osteoglycin -4.505 DAPL1 death associated protein like 1 -4.491 C10orf105 chromosome 10 open reading frame 105 -4.491 -
Hepatocyte Growth Factor Activator Inhibitor Type 1 (Hai-1/Spint1) Is a Suppressor of Intestinal Tumorigenesis
Author Manuscript Published OnlineFirst on February 27, 2013; DOI: 10.1158/0008-5472.CAN-12-3337 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Hepatocyte growth factor activator inhibitor type 1 (Hai-1/Spint1) is a suppressor of intestinal tumorigenesis Shinri Hoshiko,*,# Makiko Kawaguchi,* Tsuyoshi Fukushima,* Yukihiro Haruyama,* Kenji Yorita,* Hiroyuki Tanaka,* Motoharu Seiki,‡ Haruhiko Inatsu,# Kazuo Kitamura# and Hiroaki Kataoka* *Section of Oncopathology and Regenerative Biology, Department of Pathology and #Section of Circulatory and Body Fluid Regulation, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan; ‡Division of Cancer Cell Research, Institute of Medical Science, The University of Tokyo, Tokyo, Japan. S.H. and M.K. contributed equally to this study Running title: HAI-1 suppresses intestinal tumorigenesis Key words: HAI-1, carcinogenesis, colon cancer, hepatocyte growth factor, epithelial integrity Financial support: This work was supported by Grant-in-Aid for Scientific Research no. 24390099 (H.K.) and no. 23790250 (M.K.) from the Ministry of Education, Science, Sports and Culture, Japan. Corresponding author: Hiroaki Kataoka, Section of Oncopathology and Regenerative Biology, Department of Pathology, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan. Phone, +81-985-852809; Fax, +81-985-856003; E-mail, [email protected] 1 Downloaded from cancerres.aacrjournals.org on September 28, 2021. © 2013 American Association for Cancer Research. Author Manuscript Published OnlineFirst on February 27, 2013; DOI: 10.1158/0008-5472.CAN-12-3337 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. -
SPINT1) by Transcription Published: Xx Xx Xxxx Factor CDX2 E
www.nature.com/scientificreports OPEN Intestinal regulation of suppression of tumorigenicity 14 (ST14) and serine peptidase inhibitor, Kunitz Received: 5 April 2018 Accepted: 23 July 2018 type -1 (SPINT1) by transcription Published: xx xx xxxx factor CDX2 E. Thomas Danielsen 1,2, Anders Krüger Olsen2, Mehmet Coskun3, Annika W. Nonboe2, Sylvester Larsen 1,4, Katja Dahlgaard1, Eric Paul Bennett5, Cathy Mitchelmore1, Lotte Katrine Vogel2 & Jesper Thorvald Troelsen 1 The type II membrane-anchored serine protease, matriptase, encoded by suppression of tumorgenicity-14 (ST14) regulates the integrity of the intestinal epithelial barrier in concert with its inhibitor, HAI-1 encoded by serine peptidase inhibitor, Kunitz type -1 (SPINT1). The balance of the protease/inhibitor gene expression ratio is vital in preventing the oncogenic potential of matriptase. The intestinal cell lineage is regulated by a transcriptional regulatory network where the tumor suppressor, Caudal homeobox 2 (CDX2) is considered to be an intestinal master transcription factor. In this study, we show that CDX2 has a dual function in regulating both ST14 and SPINT1, gene expression in intestinal cells. We fnd that CDX2 is not required for the basal ST14 and SPINT1 gene expression; however changes in CDX2 expression afects the ST14/SPINT1 mRNA ratio. Exploring CDX2 ChIP-seq data from intestinal cell lines, we identifed genomic CDX2-enriched enhancer elements for both ST14 and SPINT1, which regulate their corresponding gene promoter activity. We show that CDX2 displays both repressive and enhancing regulatory abilities in a cell specifc manner. Together, these data reveal new insight into transcriptional mechanisms controlling the intestinal matriptase/inhibitor balance. -
Human Pluripotent Stem Cells As a Model of Trophoblast Differentiation in Both Normal Development and Disease
Human pluripotent stem cells as a model of trophoblast differentiation in both normal development and disease Mariko Horiia,b,1, Yingchun Lia,b,1, Anna K. Wakelanda,b,1, Donald P. Pizzoa, Katharine K. Nelsona,b, Karen Sabatinib,c, Louise Chang Laurentb,c, Ying Liud,e,f, and Mana M. Parasta,b,2 aDepartment of Pathology, University of California, San Diego, La Jolla, CA 92093; bSanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093; cDepartment of Reproductive Medicine, University of California, San Diego, La Jolla, CA 92093; dDepartment of Neurosurgery, Center for Stem Cell and Regenerative Medicine, University of Texas Health Sciences Center, Houston, TX 77030; eThe Senator Lloyd and B. A. Bentsen Center for Stroke Research, University of Texas Health Sciences Center, Houston, TX 77030; and fThe Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Sciences Center, Houston, TX 77030 Edited by R. Michael Roberts, University of Missouri–Columbia, Columbia, MO, and approved May 25, 2016 (received for review March 24, 2016) Trophoblast is the primary epithelial cell type in the placenta, a Elf5 (Ets domain transcription factor) and Eomes (Eomeso- transient organ required for proper fetal growth and develop- dermin), also have been shown to be required for maintenance of ment. Different trophoblast subtypes are responsible for gas/nutrient the TSC fate in the mouse (8, 9). exchange (syncytiotrophoblasts, STBs) and invasion and maternal Significantly less is known about TE specification and the TSC vascular remodeling (extravillous trophoblasts, EVTs). Studies of niche in the human embryo (10, 11). -
Messages from the Placentae Across Multiple Species a 50 Years
Placenta 84 (2019) 14–27 Contents lists available at ScienceDirect Placenta journal homepage: www.elsevier.com/locate/placenta Messages from the placentae across multiple species: A 50 years exploration T Hiroaki Soma Saitama Medical University, Japan ARTICLE INFO ABSTRACT Keywords: This review explores eight aspects of placentation in multiple mammalian. Gestational trophoblastic disease 1) Specialities of gestational trophoblastic disease. SUA(Single umbilical artery) 2) Clinical significance of single umbilical artery (SUA) syndrome. DIC(Disseminated intravascular coagulation) in 3) Pulmonary trophoblast embolism in pregnant chinchillas and DIC in pregnant giant panda. giant panda 4) Genetics status and placental behaviors during Japanese serow and related antelopes. Placentation in Japanese serow 5) Specific living style and placentation of the Sloth and Proboscis monkey. Hydatidiform mole in chimpanzee Placentation in different living elephant 6) Similarities of placental structures between human and great apes. Manatee and hyrax 7) Similarities of placental forms in elephants, manatees and rock hyrax with different living styles. Specific placental findings of Himalayan people 8) Specialities of placental pathology in Himalayan mountain people. Conclusions: It was taught that every mammalian species held on placental forms applied to different environ- mental life for their infants, even though their gestational lengths were different. 1. Introduction of effective chemotherapeutic agents. In 1959, I was fortunate tore- ceive an invitation from Prof. Kurt Benirschke at the Boston Lying-in Last October, Scientific American published a special issue about a Hospital. Before that, I had written to Prof. Arthur T. Hertig, Chairman baby's first organ, the placenta [1]. It is full of surprises and amazing of Pathology, Harvard Medical School, asking to study human tropho- science. -
Cellular and Molecular Signatures in the Disease Tissue of Early
Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of