Abnormal Expression of Pappa2 Gene May Indirectly Affect Mouse Hip Development Through the IGF Signaling Pathway
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Gene Expression Profiling of Corpus Luteum Reveals the Importance Of
bioRxiv preprint doi: https://doi.org/10.1101/673558; this version posted February 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. 1 Gene expression profiling of corpus luteum reveals the 2 importance of immune system during early pregnancy in 3 domestic sheep. 4 Kisun Pokharel1, Jaana Peippo2 Melak Weldenegodguad1, Mervi Honkatukia2, Meng-Hua Li3*, Juha 5 Kantanen1* 6 1 Natural Resources Institute Finland (Luke), Jokioinen, Finland 7 2 Nordgen – The Nordic Genetic Resources Center, Ås, Norway 8 3 College of Animal Science and Technology, China Agriculture University, Beijing, China 9 * Correspondence: MHL, [email protected]; JK, [email protected] 10 Abstract: The majority of pregnancy loss in ruminants occurs during the preimplantation stage, which is thus 11 the most critical period determining reproductive success. While ovulation rate is the major determinant of 12 litter size in sheep, interactions among the conceptus, corpus luteum and endometrium are essential for 13 pregnancy success. Here, we performed a comparative transcriptome study by sequencing total mRNA from 14 corpus luteum (CL) collected during the preimplantation stage of pregnancy in Finnsheep, Texel and F1 15 crosses, and mapping the RNA-Seq reads to the latest Rambouillet reference genome. A total of 21,287 genes 16 were expressed in our dataset. Highly expressed autosomal genes in the CL were associated with biological 17 processes such as progesterone formation (STAR, CYP11A1, and HSD3B1) and embryo implantation (eg. -
Gene Ontology Functional Annotations and Pleiotropy
Network based analysis of genetic disease associations Sarah Gilman Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2013 Sarah Gilman All Rights Reserved ABSTRACT Network based analysis of genetic disease associations Sarah Gilman Despite extensive efforts and many promising early findings, genome-wide association studies have explained only a small fraction of the genetic factors contributing to common human diseases. There are many theories about where this “missing heritability” might lie, but increasingly the prevailing view is that common variants, the target of GWAS, are not solely responsible for susceptibility to common diseases and a substantial portion of human disease risk will be found among rare variants. Relatively new, such variants have not been subject to purifying selection, and therefore may be particularly pertinent for neuropsychiatric disorders and other diseases with greatly reduced fecundity. Recently, several researchers have made great progress towards uncovering the genetics behind autism and schizophrenia. By sequencing families, they have found hundreds of de novo variants occurring only in affected individuals, both large structural copy number variants and single nucleotide variants. Despite studying large cohorts there has been little recurrence among the genes implicated suggesting that many hundreds of genes may underlie these complex phenotypes. The question -
A Systems-Genetics Analyses of Complex Phenotypes
A systems-genetics analyses of complex phenotypes A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 2015 David Ashbrook Table of contents Table of contents Table of contents ............................................................................................... 1 Tables and figures ........................................................................................... 10 General abstract ............................................................................................... 14 Declaration ....................................................................................................... 15 Copyright statement ........................................................................................ 15 Acknowledgements.......................................................................................... 16 Chapter 1: General introduction ...................................................................... 17 1.1 Overview................................................................................................... 18 1.2 Linkage, association and gene annotations .............................................. 20 1.3 ‘Big data’ and ‘omics’ ................................................................................ 22 1.4 Systems-genetics ..................................................................................... 24 1.5 Recombinant inbred (RI) lines and the BXD .............................................. 25 Figure 1.1: -
Copy Number Variation Distribution in Six Monozygotic Twin Pairs Discordant for Schizophrenia
Twin Research and Human Genetics Volume 17 Number 2 pp. 108–120 C The Authors 2014 doi:10.1017/thg.2014.6 Copy Number Variation Distribution in Six Monozygotic Twin Pairs Discordant for Schizophrenia Christina A. Castellani,1 Zain Awamleh,1 Melkaye G. Melka,1 Richard L. O’Reilly,2 and Shiva M. Singh1 1Department of Biology, The University of Western Ontario, London, Ontario, Canada 2Department of Psychiatry, The University of Western Ontario, London, Ontario, Canada We have evaluated copy number variants (CNVs) in six monozygotic twin pairs discordant for schizophre- nia. The data from Affymetrix R Human SNP 6.0 arraysTM were analyzed using Affymetrix R Genotyping ConsoleTM , Partek R Genomics SuiteTM , PennCNV, and Golden Helix SVSTM . This yielded both program- specific and overlapping results. Only CNVs called by Affymetrix Genotyping Console, Partek Genomics Suite, and PennCNV were used in further analysis. This analysis included an assessment of calls in each of the six twin pairs towards identification of unique CNVs in affected and unaffected co-twins. Real time polymerase chain reaction (PCR) experiments confirmed one CNV loss at 7q11.21 that was found in the affected patient but not in the unaffected twin. The results identified CNVs and genes that were previously implicated in mental abnormalities in four of the six twin pairs. It included PYY (twin pairs 1 and 5), EPHA3 (twin pair 3), KIAA1211L (twin pair 4), and GPR139 (twin pair 5). They represent likely candidate genes and CNVs for the discordance of four of the six monozygotic twin pairs for this heterogeneous neurodevelop- mental disorder. -
Identification of Neoepitopes Recognized by Tumor-Infiltrating Lymphocytes (Tils) from Patients with Glioma
www.oncotarget.com Oncotarget, 2018, Vol. 9, (No. 28), pp: 19469-19480 Research Paper: Immunology Identification of neoepitopes recognized by tumor-infiltrating lymphocytes (TILs) from patients with glioma Davide Valentini1, Martin Rao2, Qingda Meng2, Anna von Landenberg2, Jiri Bartek Jr3,4, Georges Sinclair4, Georgia Paraschoudi2, Elke Jäger5, Inti Harvey-Peredo4, Ernest Dodoo4 and Markus Maeurer1,2,5 1Centre for Allogeneic Stem Cell Transplantation (CAST), Karolinska University Hospital Huddinge, Stockholm, Sweden 2Therapeutic Immunology Unit (TIM), Department of Laboratory Medicine (LABMED), Karolinska Institutet, Stockholm, Sweden 3Department of Neurosurgery, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark 4Department of Neurosurgery, Karolinska University Hospital, Stockholm, Sweden 5 Krankenhaus Nordwest, Division of Oncology and Hematology, Frankfurt, Germany Correspondence to: Markus Maeurer, email: [email protected] Keywords: tumor-infiltrating lymphocytes; immunotherapy; neoepitopes; glioblastoma; interferon gamma; Immunology Received: September 11, 2017 Accepted: February 24, 2018 Published: April 13, 2018 Copyright: Valentini et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Neoepitope-specific T-cell responses have been shown to induce durable clinical responses in patients with advanced cancers. We explored the recognition patterns of tumor-infiltrating T lymphocytes (TILs) from patients with glioblastoma multiforme (GBM), the most fatal form of tumors of the central nervous system. Whole-genome sequencing was used for generating DNA sequences representing the entire spectrum of ‘private’ somatic mutations in GBM tumors from five patients, followed by 15-mer peptide prediction and subsequent peptide synthesis. -
1 PAPPA2, an Enzyme That Cleaves an Insulin-Like Growth Factor Binding
Genetics: Published Articles Ahead of Print, published on May 15, 2006 as 10.1534/genetics.106.057513 PAPPA2, an enzyme that cleaves an insulin-like growth factor binding protein, is a candidate gene for a QTL affecting body size in mice Julian K. Christians*,1 , Andreas Hoeflich† and Peter D. Keightley* * University of Edinburgh, Institute of Evolutionary Biology, School of Biological Sciences, Edinburgh, EH9 3JT, UK † Ludwig-Maximilians Universitaet, Institute of Molecular Breeding and Biotechnology, D- 81377 Munich, Germany 1 Present address: Simon Fraser University, Biological Sciences, Burnaby, BC, V5A 1S6, Canada 1 Running head: PAPPA2 is a candidate QTL for growth Key words: quantitative trait locus (QTL), growth, insulin-like growth factor-binding protein, pregnancy-associated plasma protein-A2 (PAPPA2) Corresponding author: Julian Christians Biological Sciences 8888 University Drive Simon Fraser University Burnaby, BC V5A 1S6 CANADA Voice: (604) 291-5619 Fax: (604) 291-3496 Email: [email protected] 2 ABSTRACT Identifying genes responsible for quantitative variation remains a major challenge. We previously identified a quantitative trait locus (QTL) affecting body size that segregated between two inbred strains of mice. By fine-mapping, we have refined the location of this QTL to a genomic region containing only four protein-coding genes. One of these genes, PAPPA2, is a strong candidate because it codes for an enzyme that cleaves insulin-like growth factor-binding protein 5 (IGFBP-5), an important stimulator of bone formation. Among littermates that segregate only for the four-gene region, we show that the QTL has a significant effect on the circulating levels of IGFBP-5 and IGFBP-3 (the latter subject to limited degradation by PAPPA2), but not on levels of IGFBP-2 and IGFBP-4, which are not cleaved by PAPPA2. -
Systems Genetics in Diversity Outbred Mice Inform BMD GWAS and Identify Determinants of Bone Strength
ARTICLE https://doi.org/10.1038/s41467-021-23649-0 OPEN Systems genetics in diversity outbred mice inform BMD GWAS and identify determinants of bone strength Basel M. Al-Barghouthi 1,2,8, Larry D. Mesner1,3,8, Gina M. Calabrese1,8, Daniel Brooks4, Steven M. Tommasini 5, Mary L. Bouxsein 4, Mark C. Horowitz5, Clifford J. Rosen 6, Kevin Nguyen1, ✉ Samuel Haddox2, Emily A. Farber1, Suna Onengut-Gumuscu 1,3, Daniel Pomp7 & Charles R. Farber 1,2,3 1234567890():,; Genome-wide association studies (GWASs) for osteoporotic traits have identified over 1000 associations; however, their impact has been limited by the difficulties of causal gene iden- tification and a strict focus on bone mineral density (BMD). Here, we use Diversity Outbred (DO) mice to directly address these limitations by performing a systems genetics analysis of 55 complex skeletal phenotypes. We apply a network approach to cortical bone RNA-seq data to discover 66 genes likely to be causal for human BMD GWAS associations, including the genes SERTAD4 and GLT8D2. We also perform GWAS in the DO for a wide-range of bone traits and identify Qsox1 as a gene influencing cortical bone accrual and bone strength. In this work, we advance our understanding of the genetics of osteoporosis and highlight the ability of the mouse to inform human genetics. 1 Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA, USA. 2 Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, USA. 3 Department of Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, VA, USA. -
Rare Cnvs Provide Novel Insights Into the Molecular Basis of GH and IGF-1 Insensitivity
6 183 E Cottrell and others CNVs in GH and IGF-1 183:6 581–595 Clinical Study insensitivity Rare CNVs provide novel insights into the molecular basis of GH and IGF-1 insensitivity Emily Cottrell1, Claudia P Cabrera2,3, Miho Ishida4, Sumana Chatterjee1, James Greening5, Neil Wright6, Artur Bossowski7, Leo Dunkel1, Asma Deeb8, Iman Al Basiri9, Stephen J Rose10, Avril Mason11, Susan Bint12, Joo Wook Ahn13, Vivian Hwa14, Louise A Metherell1, Gudrun E Moore4 and Helen L Storr1 1Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine & Dentistry, Queen Mary University of London, London, UK, 2Centre for Translational Bioinformatics, Queen Mary University of London, London, UK, 3NIHR Barts Cardiovascular Biomedical Research Centre, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK, 4University College London, Great Ormond Street Institute of Child Health, London, UK, 5University Hospitals of Leicester NHS Trust, Leicester, UK, 6The University of Sheffield Faculty of Medicine, Dentistry and Health, Sheffield, UK, 7Department of Pediatrics, Endocrinology and Diabetes with a Cardiology Unit, Medical University of Bialystok, Bialystok, Poland, 8Paediatric Endocrinology Department, Mafraq Hospital, Abu Dhabi, United Arab Emirates, 9Mubarak Al-kabeer Hospital, Jabriya, Kuwait, 10University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK, 11Royal Correspondence Hospital for Children, Glasgow, UK, 12Viapath, Guy’s Hospital, London, UK, 13Addenbrookes Hospital, Cambridge, UK, should be addressed and 14Cincinnati Center for Growth Disorders, Division of Endocrinology, Cincinnati Children’s Hospital Medical to H L Storr Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA Email [email protected] Abstract Objective: Copy number variation (CNV) has been associated with idiopathic short stature, small for gestational age and Silver-Russell syndrome (SRS). -
Genome-Wide Association Study of Perioperative Myocardial Infarction After Coronary Artery Bypass Surgery
Open Access Research BMJ Open: first published as 10.1136/bmjopen-2014-006920 on 6 May 2015. Downloaded from Genome-wide association study of perioperative myocardial infarction after coronary artery bypass surgery Miklos D Kertai,1 Yi-Ju Li,2,3 Yen-Wei Li,2 Yunqi Ji,2 John Alexander,4,5 Mark F Newman,1,5 Peter K Smith,6 Diane Joseph,5 Joseph P Mathew,1 Mihai V Podgoreanu,1,5 for the Duke Perioperative Genetics and Safety Outcomes (PEGASUS) Investigative Team To cite: Kertai MD, Li Y-J, ABSTRACT et al Strengths and limitations of this study Li Y-W, . Genome-wide Objectives: Identification of patient subpopulations association study susceptible to develop myocardial infarction (MI) or, ▪ of perioperative myocardial This is the first genome-wide association study conversely, those displaying either intrinsic infarction after coronary of perioperative myocardial infarction, using pro- artery bypass surgery. BMJ cardioprotective phenotypes or highly responsive to spective cohorts of cardiac surgical patients, Open 2015;5:e006920. protective interventions remain high-priority knowledge standard definitions of the primary phenotype doi:10.1136/bmjopen-2014- gaps. We sought to identify novel common genetic and full adjustment for non-genetic risk factors. 006920 variants associated with perioperative MI in patients ▪ We conducted comprehensive and complemen- undergoing coronary artery bypass grafting using tary single marker and pathway-based genome- ▸ Prepublication history and genome-wide association methodology. wide association analyses. supplementary files are Setting: 107 secondary and tertiary cardiac surgery ▪ The study is powered to detect relatively large available. To view please visit centres across the USA. -
Large-Scale in Silico Mapping of Complex Quantitative Traits in Inbred Mice Pengyuan Liu Washington University School of Medicine in St
Washington University School of Medicine Digital Commons@Becker Open Access Publications 2007 Large-scale in silico mapping of complex quantitative traits in inbred mice Pengyuan Liu Washington University School of Medicine in St. Louis Haris Vikis Washington University School of Medicine in St. Louis Yan Lu Washington University School of Medicine in St. Louis Daolong Wang Washington University School of Medicine in St. Louis Ming You Washington University School of Medicine in St. Louis Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Part of the Medicine and Health Sciences Commons Recommended Citation Liu, Pengyuan; Vikis, Haris; Lu, Yan; Wang, Daolong; and You, Ming, ,"Large-scale in silico mapping of complex quantitative traits in inbred mice." PLoS One.,. e651. (2007). https://digitalcommons.wustl.edu/open_access_pubs/874 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Large-Scale In Silico Mapping of Complex Quantitative Traits in Inbred Mice Pengyuan Liu, Haris Vikis, Yan Lu, Daolong Wang, Ming You* Department of Surgery and the Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America Understanding the genetic basis of common disease and disease-related quantitative traits will aid in the development of diagnostics and therapeutics. The processs of gene discovery can be sped up by rapid and effective integration of well-defined mouse genome and phenome data resources. We describe here an in silico gene-discovery strategy through genome-wide association (GWA) scans in inbred mice with a wide range of genetic variation. -
Gene Expression Profiling of Corpus Luteum Reveals Important
G C A T T A C G G C A T genes Article Gene Expression Profiling of Corpus luteum Reveals Important Insights about Early Pregnancy in Domestic Sheep Kisun Pokharel 1 , Jaana Peippo 2, Melak Weldenegodguad 1 , Mervi Honkatukia 3, Meng-Hua Li 4,* and Juha Kantanen 2,* 1 Natural Resources, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland; kisun.pokharel@luke.fi (K.P.); melak.weldenegodguad@luke.fi (M.W.) 2 Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland; jaana.peippo@luke.fi 3 NordGen—The Nordic Genetic Resources Center, 1432 Ås, Norway; [email protected] 4 College of Animal Science and Technology, China Agricultural University, Beijing 100193, China * Correspondence: [email protected] (M.-H.L.); juha.kantanen@luke.fi (J.K.); Tel.: +358-295-326-210 (J.K.) Received: 2 March 2020; Accepted: 8 April 2020; Published: 10 April 2020 Abstract: The majority of pregnancy loss in ruminants occurs during the preimplantation stage, which is thus the most critical period determining reproductive success. Here, we performed a comparative transcriptome study by sequencing total mRNA from corpus luteum (CL) collected during the preimplantation stage of pregnancy in Finnsheep, Texel and F1 crosses. A total of 21,287 genes were expressed in our data. Highly expressed autosomal genes in the CL were associated with biological processes such as progesterone formation (STAR, CYP11A1, and HSD3B1) and embryo implantation (e.g., TIMP1, TIMP2 and TCTP). Among the list of differentially expressed genes, sialic acid-binding immunoglobulin (Ig)-like lectins (SIGLEC3, SIGLEC14, SIGLEC8), ribosomal proteins (RPL17, RPL34, RPS3A, MRPS33) and chemokines (CCL5, CCL24, CXCL13, CXCL9) were upregulated in Finnsheep, while four multidrug resistance-associated proteins (MRPs) were upregulated in Texel ewes. -
Systems Genetics Analyses in Diversity Outbred Mice
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.24.169839; this version posted March 14, 2021. 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 4.0 International license. 1 Systems genetics analyses in Diversity Outbred mice inform 2 human bone mineral density GWAS and identify Qsox1 as a 3 novel determinant of bone strength 4 5 6 Basel M. Al-Barghouthi1,2,8, Larry D. Mesner1,6,8, Gina M. Calabrese1,8, Daniel Brooks3, 7 Steven M. Tommasini4, Mary L. Bouxsein3, Mark C. Horowitz4, Clifford J. Rosen5, Kevin 8 Nguyen1, Samuel HaDDox2, Emily A. Farber1, Suna Onengut-Gumuscu1,6, Daniel Pomp7 9 anD Charles R. Farber1,2,6 10 11 1 Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22908 12 2 Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, 13 Charlottesville, VA 22908 14 3 Center for Advanced Orthopedic Studies, Beth Israel Deaconess Medical Center, Department of 15 Orthopedic Surgery, Harvard Medical School, Boston, MA 02215 16 4 Department of Orthopaedics and Rehabilitation, Yale School of Medicine, New Haven, CT 06520 17 5 Maine Medical Center Research Institute, 81 Research Drive, Scarborough, ME 04074 18 6 Department of Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, VA 19 22908 20 7 Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599 21 8 Contributed equally to this work 22 23 24 25 26 27 28 29 30 Correspondence to: 31 32 Charles R.