Hirschsprung's Disease
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Core Transcriptional Regulatory Circuitries in Cancer
Oncogene (2020) 39:6633–6646 https://doi.org/10.1038/s41388-020-01459-w REVIEW ARTICLE Core transcriptional regulatory circuitries in cancer 1 1,2,3 1 2 1,4,5 Ye Chen ● Liang Xu ● Ruby Yu-Tong Lin ● Markus Müschen ● H. Phillip Koeffler Received: 14 June 2020 / Revised: 30 August 2020 / Accepted: 4 September 2020 / Published online: 17 September 2020 © The Author(s) 2020. This article is published with open access Abstract Transcription factors (TFs) coordinate the on-and-off states of gene expression typically in a combinatorial fashion. Studies from embryonic stem cells and other cell types have revealed that a clique of self-regulated core TFs control cell identity and cell state. These core TFs form interconnected feed-forward transcriptional loops to establish and reinforce the cell-type- specific gene-expression program; the ensemble of core TFs and their regulatory loops constitutes core transcriptional regulatory circuitry (CRC). Here, we summarize recent progress in computational reconstitution and biologic exploration of CRCs across various human malignancies, and consolidate the strategy and methodology for CRC discovery. We also discuss the genetic basis and therapeutic vulnerability of CRC, and highlight new frontiers and future efforts for the study of CRC in cancer. Knowledge of CRC in cancer is fundamental to understanding cancer-specific transcriptional addiction, and should provide important insight to both pathobiology and therapeutics. 1234567890();,: 1234567890();,: Introduction genes. Till now, one critical goal in biology remains to understand the composition and hierarchy of transcriptional Transcriptional regulation is one of the fundamental mole- regulatory network in each specified cell type/lineage. -
An Order Estimation Based Approach to Identify Response Genes
AN ORDER ESTIMATION BASED APPROACH TO IDENTIFY RESPONSE GENES FOR MICRO ARRAY TIME COURSE DATA A Thesis Presented to The Faculty of Graduate Studies of The University of Guelph by ZHIHENG LU In partial fulfilment of requirements for the degree of Doctor of Philosophy September, 2008 © Zhiheng Lu, 2008 Library and Bibliotheque et 1*1 Archives Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington Ottawa ON K1A0N4 Ottawa ON K1A0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-47605-5 Our file Notre reference ISBN: 978-0-494-47605-5 NOTICE: AVIS: The author has granted a non L'auteur a accorde une licence non exclusive exclusive license allowing Library permettant a la Bibliotheque et Archives and Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par Plntemet, prefer, telecommunication or on the Internet, distribuer et vendre des theses partout dans loan, distribute and sell theses le monde, a des fins commerciales ou autres, worldwide, for commercial or non sur support microforme, papier, electronique commercial purposes, in microform, et/ou autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in et des droits moraux qui protege cette these. this thesis. Neither the thesis Ni la these ni des extraits substantiels de nor substantial extracts from it celle-ci ne doivent etre imprimes ou autrement may be printed or otherwise reproduits sans son autorisation. -
Bhagwan Moorjani, MD, FAAP, FAAN • Requires Knowledge of Normal CNS Developmental (I.E
1/16/2012 Neuroimaging in Childhood • Neuroimaging issues are distinct from Pediatric Neuroimaging in adults Neurometabolic-degenerative disorder • Sedation/anesthesia and Epilepsy • Motion artifacts Bhagwan Moorjani, MD, FAAP, FAAN • Requires knowledge of normal CNS developmental (i.e. myelin maturation) • Contrast media • Parental anxiety Diagnostic Approach Neuroimaging in Epilepsy • Age of onset • Peak incidence in childhood • Static vs Progressive • Occurs as a co-morbid condition in many – Look for treatable causes pediatric disorders (birth injury, – Do not overlook abuse, Manchausen if all is negative dysmorphism, chromosomal anomalies, • Phenotype presence (syndromic, HC, NCS, developmental delays/regression) systemic involvement) • Predominant symptom (epilepsy, DD, • Many neurologic disorders in children weakness/motor, psychomotor regression, have the same chief complaint cognitive/dementia) 1 1/16/2012 Congenital Malformation • Characterized by their anatomic features • Broad categories: based on embryogenesis – Stage 1: Dorsal Induction: Formation and closure of the neural tube. (Weeks 3-4) – Stage 2: Ventral Induction: Formation of the brain segments and face. (Weeks 5-10) – Stage 3: Migration and Histogenesis: (Months 2-5) – Stage 4: Myelination: (5-15 months; matures by 3 years) Dandy Walker Malformation Dandy walker • Criteria: – high position of tentorium – dysgenesis/agenesis of vermis – cystic dilatation of fourth ventricle • commonly associated features: – hypoplasia of cerebellum – scalloping of inner table of occipital bone • associated abnormalities: – hydrocephalus 75% – dysgenesis of corpus callosum 25% – heterotropia 10% 2 1/16/2012 Etiology of Epilepsy: Developmental and Genetic Classification of Gray Matter Heterotropia Cortical Dysplasia 1. Secondary to abnormal neuronal and • displaced masses of nerve cells • Subependymal glial proliferation/apoptosis (gray matter) heterotropia (most • most common: small nest common) 2. -
Table 2. Significant
Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Preconception Carrier Screening by Genome Sequencing: Results from the Clinical Laboratory
The American Journal of Human Genetics, Volume 102 Supplemental Data Preconception Carrier Screening by Genome Sequencing: Results from the Clinical Laboratory Sumit Punj, Yassmine Akkari, Jennifer Huang, Fei Yang, Allison Creason, Christine Pak, Amiee Potter, Michael O. Dorschner, Deborah A. Nickerson, Peggy D. Robertson, Gail P. Jarvik, Laura M. Amendola, Jennifer Schleit, Dana Kostiner Simpson, Alan F. Rope, Jacob Reiss, Tia Kauffman, Marian J. Gilmore, Patricia Himes, Benjamin Wilfond, Katrina A.B. Goddard, and C. Sue Richards Supplemental Note: Clinical Report Carrier Results: Four Known Pathogenic Variants Detected. Gene Inheritance Disease Prevalence Variant Classification Pendred Syndrome/ Non- syndromic Autosomal Hearing Loss A c.1246A>C, SLC26A4 1/500 Pathogenic Recessive DFNB4 with (p.Thr416Pro) enlarged vestibular aqueduct Autosomal Spastic ++ c.1045G>A, SPG7 2-6/100,000 Pathogenic Recessive Paraplegia 7 (p.Gly349Ser) 3.7 Autosomal Alpha +++ -α HBA2 1-5/10,000 Pathogenic Recessive Thalassemia (α+- thalassemia) Autosomal Hereditary 1/200 – c.845G>A HFE Pathogenic Recessive Hemochromatosis 1/1000+ (p.Cys282Tyr) +: GeneReviews; ++: Genetics Home Reference; +++: orphan.net – varies with population; A- Generalized prevalence of all deafness and hearing loss Interpretation: A sample from this individual was referred to our laboratory for analysis of Next-Generation Genome Sequencing (NGS) and Sanger confirmation of variants identified in carrier screening for: (1) conditions with significantly shortened lifespan; (2) serious conditions; (3) mild conditions; (4) conditions with unpredictable outcomes: and (5) conditions that begin as adults. One known heterozygous missense variant, c.1246A>C (p.Thr416Pro) (NM_000441.1), was detected in exon 10 of the SLC26A4 gene of this individual by NGS. -
Sequence Analysis of Familial Neurodevelopmental Disorders
SEQUENCE ANALYSIS OF FAMILIAL NEURODEVELOPMENTAL DISORDERS by Joseph Mark Tilghman A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland December 2020 © 2020 Joseph Tilghman All Rights Reserved Abstract: In the practice of human genetics, there is a gulf between the study of Mendelian and complex inheritance. When diagnosis of families affected by presumed monogenic syndromes is undertaken by genomic sequencing, these families are typically considered to have been solved only when a single gene or variant showing apparently Mendelian inheritance is discovered. However, about half of such families remain unexplained through this approach. On the other hand, common regulatory variants conferring low risk of disease still predominate our understanding of individual disease risk in complex disorders, despite rapidly increasing access to rare variant genotypes through sequencing. This dissertation utilizes primarily exome sequencing across several developmental disorders (having different levels of genetic complexity) to investigate how to best use an individual’s combination of rare and common variants to explain genetic risk, phenotypic heterogeneity, and the molecular bases of disorders ranging from those presumed to be monogenic to those known to be highly complex. The study described in Chapter 2 addresses putatively monogenic syndromes, where we used exome sequencing of four probands having syndromic neurodevelopmental disorders from an Israeli-Arab founder population to diagnose recessive and dominant disorders, highlighting the need to consider diverse modes of inheritance and phenotypic heterogeneity. In the study described in Chapter 3, we address the case of a relatively tractable multifactorial disorder, Hirschsprung disease. -
Generalized Hypertrichosis
Letters to the Editor case of female. Ambras syndrome is a type of universal Generalized hypertrichosis affecting the vellus hair, where there is uniform overgrowth of hair over the face and external hypertrichosis ear with or without dysmorphic facies.[3] Patients with Gingival fi bromaatosis also have generalized hypertrichosis Sir, especially on the face.[4] Congenital hypertrichosis can A 4-year-old girl born out of non-consanguinous marriage occur due to fetal alcohol syndrome and fetal hydentoin presented with generalized increase in body hair noticed syndrome.[5] Prepubertal hypertrichosis is seen in otherwise since birth. None of the other family members were healthy infants and children. There is involvement of affected. Hair was pigmented and soft suggesting vellus hair. face back and extremities Distribution of hair shows an There was generalized increase in body hair predominantly inverted fi r-tree pattern on the back. More commonly seen affecting the back of trunk arms and legs [Figures 1 and 2]. in Mediterranean and South Asian descendants.[6] There is Face was relatively spared except for fore head. Palms and soles were spared. Scalp hair was normal. Teeth and nail usually no hormonal alterations. Various genodermatosis were normal. There was no gingival hypertrophy. No other associated with hypertrichosis as the main or secondary skeletal or systemic abnormalities were detected clinically. diagnostic symptom are: Routine blood investigations were normal. Hormonal Lipoatrophy (Lawrernce Seip syndrome) study was within normal limit for her age. With this Cornelia de Lange syndrome clinical picture of generalized hypertrichosis with no other Craniofacial dysostosis associated anomalies a diagnosis of universal hypertrichosis Winchester syndrome was made. -
The Genetic Heterogeneity of Brachydactyly Type A1: Identifying the Molecular Pathways
The genetic heterogeneity of brachydactyly type A1: Identifying the molecular pathways Lemuel Jean Racacho Thesis submitted to the Faculty of Graduate Studies and Postdoctoral Studies in partial fulfillment of the requirements for the Doctorate in Philosophy degree in Biochemistry Specialization in Human and Molecular Genetics Department of Biochemistry, Microbiology and Immunology Faculty of Medicine University of Ottawa © Lemuel Jean Racacho, Ottawa, Canada, 2015 Abstract Brachydactyly type A1 (BDA1) is a rare autosomal dominant trait characterized by the shortening of the middle phalanges of digits 2-5 and of the proximal phalange of digit 1 in both hands and feet. Many of the brachymesophalangies including BDA1 have been associated with genetic perturbations along the BMP-SMAD signaling pathway. The goal of this thesis is to identify the molecular pathways that are associated with the BDA1 phenotype through the genetic assessment of BDA1-affected families. We identified four missense mutations that are clustered with other reported BDA1 mutations in the central region of the N-terminal signaling peptide of IHH. We also identified a missense mutation in GDF5 cosegregating with a semi-dominant form of BDA1. In two families we reported two novel BDA1-associated sequence variants in BMPR1B, the gene which codes for the receptor of GDF5. In 2002, we reported a BDA1 trait linked to chromosome 5p13.3 in a Canadian kindred (BDA1B; MIM %607004) but we did not discover a BDA1-causal variant in any of the protein coding genes within the 2.8 Mb critical region. To provide a higher sensitivity of detection, we performed a targeted enrichment of the BDA1B locus followed by high-throughput sequencing. -
Pushing the Limits of Prenatal Ultrasound: a Case of Dorsal Dermal Sinus Associated with an Overt Arnold–Chiari Malformation and a 3Q Duplication
reproductive medicine Case Report Pushing the Limits of Prenatal Ultrasound: A Case of Dorsal Dermal Sinus Associated with an Overt Arnold–Chiari Malformation and a 3q Duplication Olivier Leroij 1, Lennart Van der Veeken 2,*, Bettina Blaumeiser 3 and Katrien Janssens 3 1 Faculty of Medicine, University of Antwerp, 2610 Wilrijk, Belgium; [email protected] 2 Department of Obstetrics and Gynaecology, University Hospital Antwerp, 2650 Edegem, Belgium 3 Department of Medical Genetics, University Hospital and University of Antwerp, 2650 Edegem, Belgium; [email protected] (B.B.); [email protected] (K.J.) * Correspondence: [email protected] Abstract: We present a case of a fetus with cranial abnormalities typical of open spina bifida but with an intact spine shown on both ultrasound and fetal MRI. Expert ultrasound examination revealed a very small tract between the spine and the skin, and a postmortem examination confirmed the diagnosis of a dorsal dermal sinus. Genetic analysis found a mosaic 3q23q27 duplication in the form of a marker chromosome. This case emphasizes that meticulous prenatal ultrasound examination has the potential to diagnose even closed subtypes of neural tube defects. Furthermore, with cerebral anomalies suggesting a spina bifida, other imaging techniques together with genetic tests and measurement of alpha-fetoprotein in the amniotic fluid should be performed. Citation: Leroij, O.; Van der Veeken, Keywords: dorsal dermal sinus; Arnold–Chiari anomaly; 3q23q27 duplication; mosaic; marker chro- L.; Blaumeiser, B.; Janssens, K. mosome Pushing the Limits of Prenatal Ultrasound: A Case of Dorsal Dermal Sinus Associated with an Overt Arnold–Chiari Malformation and a 3q 1. -
Prevalence and Incidence of Rare Diseases: Bibliographic Data
Number 1 | January 2019 Prevalence and incidence of rare diseases: Bibliographic data Prevalence, incidence or number of published cases listed by diseases (in alphabetical order) www.orpha.net www.orphadata.org If a range of national data is available, the average is Methodology calculated to estimate the worldwide or European prevalence or incidence. When a range of data sources is available, the most Orphanet carries out a systematic survey of literature in recent data source that meets a certain number of quality order to estimate the prevalence and incidence of rare criteria is favoured (registries, meta-analyses, diseases. This study aims to collect new data regarding population-based studies, large cohorts studies). point prevalence, birth prevalence and incidence, and to update already published data according to new For congenital diseases, the prevalence is estimated, so scientific studies or other available data. that: Prevalence = birth prevalence x (patient life This data is presented in the following reports published expectancy/general population life expectancy). biannually: When only incidence data is documented, the prevalence is estimated when possible, so that : • Prevalence, incidence or number of published cases listed by diseases (in alphabetical order); Prevalence = incidence x disease mean duration. • Diseases listed by decreasing prevalence, incidence When neither prevalence nor incidence data is available, or number of published cases; which is the case for very rare diseases, the number of cases or families documented in the medical literature is Data collection provided. A number of different sources are used : Limitations of the study • Registries (RARECARE, EUROCAT, etc) ; The prevalence and incidence data presented in this report are only estimations and cannot be considered to • National/international health institutes and agencies be absolutely correct. -
WES Gene Package Multiple Congenital Anomalie.Xlsx
Whole Exome Sequencing Gene package Multiple congenital anomalie, version 5, 1‐2‐2018 Technical information DNA was enriched using Agilent SureSelect Clinical Research Exome V2 capture and paired‐end sequenced on the Illumina platform (outsourced). The aim is to obtain 8.1 Giga base pairs per exome with a mapped fraction of 0.99. The average coverage of the exome is ~50x. Duplicate reads are excluded. Data are demultiplexed with bcl2fastq Conversion Software from Illumina. Reads are mapped to the genome using the BWA‐MEM algorithm (reference: http://bio‐bwa.sourceforge.net/). Variant detection is performed by the Genome Analysis Toolkit HaplotypeCaller (reference: http://www.broadinstitute.org/gatk/). The detected variants are filtered and annotated with Cartagenia software and classified with Alamut Visual. It is not excluded that pathogenic mutations are being missed using this technology. At this moment, there is not enough information about the sensitivity of this technique with respect to the detection of deletions and duplications of more than 5 nucleotides and of somatic mosaic mutations (all types of sequence changes). HGNC approved Phenotype description including OMIM phenotype ID(s) OMIM median depth % covered % covered % covered gene symbol gene ID >10x >20x >30x A4GALT [Blood group, P1Pk system, P(2) phenotype], 111400 607922 101 100 100 99 [Blood group, P1Pk system, p phenotype], 111400 NOR polyagglutination syndrome, 111400 AAAS Achalasia‐addisonianism‐alacrimia syndrome, 231550 605378 73 100 100 100 AAGAB Keratoderma, palmoplantar,