1
|
Siri B, Olivieri G, Lepri FR, Poms M, Goffredo BM, Commone A, Novelli A, Häberle J, Dionisi-Vici C. Father-to-daughter transmission in late-onset OTC deficiency: an underestimated mechanism of inheritance of an X-linked disease. Orphanet J Rare Dis 2024; 19:3. [PMID: 38167094 PMCID: PMC10763478 DOI: 10.1186/s13023-023-02997-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Ornithine Transcarbamylase Deficiency (OTCD) is an X-linked urea cycle disorder characterized by acute hyperammonemic episodes. Hemizygous males are usually affected by a severe/fatal neonatal-onset form or, less frequently, by a late-onset form with milder disease course, depending on the residual enzymatic activity. Hyperammonemia can occur any time during life and patients could remain non- or mis-diagnosed due to unspecific symptoms. In heterozygous females, clinical presentation varies based on the extent of X chromosome inactivation. Maternal transmission in X-linked disease is the rule, but in late-onset OTCD, due to the milder phenotype of affected males, paternal transmission to the females is possible. So far, father-to-daughter transmission of OTCD has been reported only in 4 Japanese families. RESULTS We identified in 2 Caucasian families, paternal transmission of late-onset OTCD with severe/fatal outcome in affected males and 1 heterozygous female. Furthermore, we have reassessed the pedigrees of other published reports in 7 additional families with evidence of father-to-daughter inheritance of OTCD, identifying and listing the family members for which this transmission occurred. CONCLUSIONS Our study highlights how the diagnosis and pedigree analysis of late-onset OTCD may represent a real challenge for clinicians. Therefore, the occurrence of paternal transmission in OTCD should not be underestimated, due to the relevant implications for disease inheritance and risk of recurrence.
Collapse
Affiliation(s)
- Barbara Siri
- Division of Metabolic Diseases and Hepatology, Bambino Gesù Children's Hospital, IRCCS, Piazza S. Onofrio 4, 00165, Rome, Italy.
- Department of Paediatrics, Città della Salute e della Scienza, OIRM, University of Turin, Turin, Italy.
| | - Giorgia Olivieri
- Division of Metabolic Diseases and Hepatology, Bambino Gesù Children's Hospital, IRCCS, Piazza S. Onofrio 4, 00165, Rome, Italy
| | - Francesca Romana Lepri
- Translational Cytogenomics Research Unit, Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Martin Poms
- Division of Clinical Chemistry and Biochemistry and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Bianca Maria Goffredo
- Division of Metabolism and Metabolic Diseases Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Anna Commone
- Division of Metabolic Diseases and Hepatology, Bambino Gesù Children's Hospital, IRCCS, Piazza S. Onofrio 4, 00165, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Johannes Häberle
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Carlo Dionisi-Vici
- Division of Metabolic Diseases and Hepatology, Bambino Gesù Children's Hospital, IRCCS, Piazza S. Onofrio 4, 00165, Rome, Italy
| |
Collapse
|
2
|
Caldovic L, Ahn JJ, Andricovic J, Balick VM, Brayer M, Chansky PA, Dawson T, Edwards AC, Felsen SE, Ismat K, Jagannathan SV, Mann BT, Medina JA, Morizono T, Morizono M, Salameh S, Vashist N, Williams EC, Zhou Z, Morizono H. Datamining approaches for examining the low prevalence of N-acetylglutamate synthase deficiency and understanding transcriptional regulation of urea cycle genes. J Inherit Metab Dis 2023. [PMID: 37847851 DOI: 10.1002/jimd.12687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
Ammonia, which is toxic to the brain, is converted into non-toxic urea, through a pathway of six enzymatically catalyzed steps known as the urea cycle. In this pathway, N-acetylglutamate synthase (NAGS, EC 2.3.1.1) catalyzes the formation of N-acetylglutamate (NAG) from glutamate and acetyl coenzyme A. NAGS deficiency (NAGSD) is the rarest of the urea cycle disorders, yet is unique in that ureagenesis can be restored with the drug N-carbamylglutamate (NCG). We investigated whether the rarity of NAGSD could be due to low sequence variation in the NAGS genomic region, high NAGS tolerance for amino acid replacements, and alternative sources of NAG and NCG in the body. We also evaluated whether the small genomic footprint of the NAGS catalytic domain might play a role. The small number of patients diagnosed with NAGSD could result from the absence of specific disease biomarkers and/or short NAGS catalytic domain. We screened for sequence variants in NAGS regulatory regions in patients suspected of having NAGSD and found a novel NAGS regulatory element in the first intron of the NAGS gene. We applied the same datamining approach to identify regulatory elements in the remaining urea cycle genes. In addition to the known promoters and enhancers of each gene, we identified several novel regulatory elements in their upstream regions and first introns. The identification of cis-regulatory elements of urea cycle genes and their associated transcription factors holds promise for uncovering shared mechanisms governing urea cycle gene expression and potentially leading to new treatments for urea cycle disorders.
Collapse
Affiliation(s)
- Ljubica Caldovic
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Julie J Ahn
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Jacklyn Andricovic
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Veronica M Balick
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Mallory Brayer
- Department of Biological Sciences, The George Washington University, Washington, DC, USA
| | - Pamela A Chansky
- The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Tyson Dawson
- The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
- AMPEL BioSolutions LLC, Charlottesville, Virginia, USA
| | - Alex C Edwards
- The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
- Center for Neuroscience Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
| | - Sara E Felsen
- The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
- Center for Neuroscience Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
| | - Karim Ismat
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Sveta V Jagannathan
- The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Brendan T Mann
- Department of Microbiology, Immunology, and Tropical Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Jacob A Medina
- The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Toshio Morizono
- College of Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michio Morizono
- College of Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Shatha Salameh
- Department of Pharmacology & Physiology, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
- Sheikh Zayed Institute for Pediatric Surgical Innovation, Children's National Hospital, Washington, DC, USA
| | - Neerja Vashist
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Emily C Williams
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
- The George Washington University Cancer Center, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
| | - Zhe Zhou
- Department of Civil and Environmental Engineering, The George Washington University, Washington, DC, USA
| | - Hiroki Morizono
- Center for Genetic Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC, USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| |
Collapse
|
3
|
Ibrahim MS, Gold JI, Woodall A, Yilmaz BS, Gissen P, Stepien KM. Diagnostic and Management Issues in Patients with Late-Onset Ornithine Transcarbamylase Deficiency. CHILDREN (BASEL, SWITZERLAND) 2023; 10:1368. [PMID: 37628367 PMCID: PMC10453542 DOI: 10.3390/children10081368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023]
Abstract
Ornithine transcarbamylase deficiency (OTCD) is the most common inherited disorder of the urea cycle and, in general, is transmitted as an X-linked recessive trait. Defects in the OTC gene cause an impairment in ureagenesis, resulting in hyperammonemia, which is a direct cause of brain damage and death. Patients with late-onset OTCD can develop symptoms from infancy to later childhood, adolescence or adulthood. Clinical manifestations of adults with OTCD vary in acuity. Clinical symptoms can be aggravated by metabolic stressors or the presence of a catabolic state, or due to increased demands upon the urea. A prompt diagnosis and relevant biochemical and genetic investigations allow the rapid introduction of the right treatment and prevent long-term complications and mortality. This narrative review outlines challenges in diagnosing and managing patients with late-onset OTCD.
Collapse
Affiliation(s)
- Majitha Seyed Ibrahim
- Department of Chemical Pathology, Teaching Hospital Batticaloa, Batticaloa 30000, Sri Lanka
| | - Jessica I. Gold
- Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alison Woodall
- Adult Inherited Metabolic Diseases, Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Salford M6 8HD, UK
| | - Berna Seker Yilmaz
- Great Ormond Street Institute of Child Health, University College London, London WC1E 6BT, UK
| | - Paul Gissen
- Great Ormond Street Institute of Child Health, University College London, London WC1E 6BT, UK
- Department of Paediatric Metabolic Medicine, Great Ormond Street Hospital for Children NHS Trust, London WC1N 3JH, UK
- National Institute of Health Research, Great Ormond Street Biomedical Research Centre, London WC1N 1EH, UK
| | - Karolina M. Stepien
- Adult Inherited Metabolic Diseases, Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Salford M6 8HD, UK
- Division of Cardiovascular Sciences, University of Manchester, Manchester M13 9PL, UK
| |
Collapse
|
4
|
Goldman O, Adler LN, Hajaj E, Croese T, Darzi N, Galai S, Tishler H, Ariav Y, Lavie D, Fellus-Alyagor L, Oren R, Kuznetsov Y, David E, Jaschek R, Stossel C, Singer O, Malitsky S, Barak R, Seger R, Erez N, Amit I, Tanay A, Saada A, Golan T, Rubinek T, Sang Lee J, Ben-Shachar S, Wolf I, Erez A. Early Infiltration of Innate Immune Cells to the Liver Depletes HNF4α and Promotes Extrahepatic Carcinogenesis. Cancer Discov 2023; 13:1616-1635. [PMID: 36972357 PMCID: PMC10326600 DOI: 10.1158/2159-8290.cd-22-1062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/19/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Multiple studies have identified metabolic changes within the tumor and its microenvironment during carcinogenesis. Yet, the mechanisms by which tumors affect the host metabolism are unclear. We find that systemic inflammation induced by cancer leads to liver infiltration of myeloid cells at early extrahepatic carcinogenesis. The infiltrating immune cells via IL6-pSTAT3 immune-hepatocyte cross-talk cause the depletion of a master metabolic regulator, HNF4α, consequently leading to systemic metabolic changes that promote breast and pancreatic cancer proliferation and a worse outcome. Preserving HNF4α levels maintains liver metabolism and restricts carcinogenesis. Standard liver biochemical tests can identify early metabolic changes and predict patients' outcomes and weight loss. Thus, the tumor induces early metabolic changes in its macroenvironment with diagnostic and potentially therapeutic implications for the host. SIGNIFICANCE Cancer growth requires a permanent nutrient supply starting from early disease stages. We find that the tumor extends its effect to the host's liver to obtain nutrients and rewires the systemic and tissue-specific metabolism early during carcinogenesis. Preserving liver metabolism restricts tumor growth and improves cancer outcomes. This article is highlighted in the In This Issue feature, p. 1501.
Collapse
Affiliation(s)
- Omer Goldman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lital N Adler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Emma Hajaj
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tommaso Croese
- Department of Brain Science, Weizmann Institute of Science, Rehovot, Israel
| | - Naama Darzi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sivan Galai
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hila Tishler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yarden Ariav
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dor Lavie
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Liat Fellus-Alyagor
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Roni Oren
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Yuri Kuznetsov
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal David
- Department of System Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Rami Jaschek
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Chani Stossel
- Oncology Institute, Sheba Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Oded Singer
- Life Science Core Facility, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- Life Science Core Facility, Weizmann Institute of Science, Rehovot, Israel
| | - Renana Barak
- Oncology Division, Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Rony Seger
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Neta Erez
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ido Amit
- Department of System Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Amos Tanay
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Ann Saada
- Department of Genetics, Hadassah Medical Center, Hebrew University and Faculty of Medicine, Jerusalem, Israel
| | - Talia Golan
- Oncology Institute, Sheba Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Rubinek
- Oncology Division, Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Joo Sang Lee
- Department of Precision Medicine, School of Medicine and Department of Artificial Intelligence, Sungkyunkwan University, Suwon, Republic of Korea
| | - Shay Ben-Shachar
- Clalit Research Institute, Innovation Division, Clalit Health Services, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ido Wolf
- Oncology Division, Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Ayelet Erez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
5
|
Morova T, Ding Y, Huang CCF, Sar F, Schwarz T, Giambartolomei C, Baca S, Grishin D, Hach F, Gusev A, Freedman M, Pasaniuc B, Lack N. Optimized high-throughput screening of non-coding variants identified from genome-wide association studies. Nucleic Acids Res 2022; 51:e18. [PMID: 36546757 PMCID: PMC9943666 DOI: 10.1093/nar/gkac1198] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/19/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
The vast majority of disease-associated single nucleotide polymorphisms (SNP) identified from genome-wide association studies (GWAS) are localized in non-coding regions. A significant fraction of these variants impact transcription factors binding to enhancer elements and alter gene expression. To functionally interrogate the activity of such variants we developed snpSTARRseq, a high-throughput experimental method that can interrogate the functional impact of hundreds to thousands of non-coding variants on enhancer activity. snpSTARRseq dramatically improves signal-to-noise by utilizing a novel sequencing and bioinformatic approach that increases both insert size and the number of variants tested per loci. Using this strategy, we interrogated known prostate cancer (PCa) risk-associated loci and demonstrated that 35% of them harbor SNPs that significantly altered enhancer activity. Combining these results with chromosomal looping data we could identify interacting genes and provide a mechanism of action for 20 PCa GWAS risk regions. When benchmarked to orthogonal methods, snpSTARRseq showed a strong correlation with in vivo experimental allelic-imbalance studies whereas there was no correlation with predictive in silico approaches. Overall, snpSTARRseq provides an integrated experimental and computational framework to functionally test non-coding genetic variants.
Collapse
Affiliation(s)
- Tunc Morova
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Yi Ding
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Funda Sar
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Tommer Schwarz
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Claudia Giambartolomei
- Central RNA Lab, Istituto Italiano di Tecnologia, Genova 16163, Italy,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sylvan C Baca
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Dennis Grishin
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Faraz Hach
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada,Department of Urologic Science, University of British Columbia, Vancouver, BC V5Z 1M9, Canada
| | - Alexander Gusev
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Matthew L Freedman
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Boston, MA 02215, USA,The Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA 90095, USA,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA,Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nathan A Lack
- To whom correspondence should be addressed. Tel: +1 604 875 4411;
| |
Collapse
|
6
|
Feigenbaum A. Challenges of managing ornithine transcarbamylase deficiency in female heterozygotes. Mol Genet Metab Rep 2022; 33:100941. [PMID: 36620389 PMCID: PMC9817477 DOI: 10.1016/j.ymgmr.2022.100941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Urea cycle disorders (UCDs) are a group of rare inherited metabolic conditions caused by enzyme deficiency within the hepatic ammonia detoxification pathway. Ornithine transcarbamylase (OTC) deficiency, the most frequently occurring UCD, is an X-linked condition known to yield a vastly heterogeneous phenotype, with variable onset and presentation across the lifespan. Here, we introduce a series of 4 original cases, published as part of this special supplement, that illustrate learnings for the care of heterozygous females with OTC deficiency, including challenges with diagnosis, potential triggers of hyperammonemia, cognitive effects, and approaches to disease management, including peripartum care.
Collapse
Affiliation(s)
- Annette Feigenbaum
- Department of Pediatrics, Division of Genetics, Rady Children's Hospital-San Diego, USA,University of California, San Diego, USA,Corresponding author at: Rady Children's Hospital-San Diego, Division of Genetics, 3020 Children's Way #5031, San Diego, CA 92123, USA.
| |
Collapse
|
7
|
Hertzog A, Selvanathan A, Farnsworth E, Tchan M, Adams L, Lewis K, Tolun AA, Bennetts B, Ho G, Bhattacharya K. Intronic variants in inborn errors of metabolism: Beyond the exome. Front Genet 2022; 13:1031495. [PMID: 36561316 PMCID: PMC9763607 DOI: 10.3389/fgene.2022.1031495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Non-coding regions are areas of the genome that do not directly encode protein and were initially thought to be of little biological relevance. However, subsequent identification of pathogenic variants in these regions indicates there are exceptions to this assertion. With the increasing availability of next generation sequencing, variants in non-coding regions are often considered when no causative exonic changes have been identified. There is still a lack of understanding of normal human variation in non-coding areas. As a result, potentially pathogenic non-coding variants are initially classified as variants of uncertain significance or are even overlooked during genomic analysis. In most cases where the phenotype is non-specific, clinical suspicion is not sufficient to warrant further exploration of these changes, partly due to the magnitude of non-coding variants identified. In contrast, inborn errors of metabolism (IEMs) are one group of genetic disorders where there is often high phenotypic specificity. The clinical and biochemical features seen often result in a narrow list of diagnostic possibilities. In this context, there have been numerous cases in which suspicion of a particular IEM led to the discovery of a variant in a non-coding region. We present four patients with IEMs where the molecular aetiology was identified within non-coding regions. Confirmation of the molecular diagnosis is often aided by the clinical and biochemical specificity associated with IEMs. Whilst the clinical severity associated with a non-coding variant can be difficult to predict, obtaining a molecular diagnosis is crucial as it ends diagnostic odysseys and assists in management.
Collapse
Affiliation(s)
- Ashley Hertzog
- NSW Biochemical Genetics Service, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia,Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,*Correspondence: Ashley Hertzog,
| | - Arthavan Selvanathan
- Genetic Metabolic Disorders Service, Sydney Children’s Hospitals Network, Sydney, NSW, Australia
| | - Elizabeth Farnsworth
- Department of Molecular Genetics, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia
| | - Michel Tchan
- Department of Genetic Medicine, Westmead Hospital, Sydney, NSW, Australia
| | - Louisa Adams
- Genetic Metabolic Disorders Service, Sydney Children’s Hospitals Network, Sydney, NSW, Australia
| | - Katherine Lewis
- Genetic Metabolic Disorders Service, Sydney Children’s Hospitals Network, Sydney, NSW, Australia
| | - Adviye Ayper Tolun
- NSW Biochemical Genetics Service, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia,Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Bruce Bennetts
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,Department of Molecular Genetics, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia
| | - Gladys Ho
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,Department of Molecular Genetics, Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children’s Hospital at Westmead, Sydney, NSW, Australia
| | - Kaustuv Bhattacharya
- Disciplines of Genetic Medicine and Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia,Genetic Metabolic Disorders Service, Sydney Children’s Hospitals Network, Sydney, NSW, Australia
| |
Collapse
|
8
|
Soriano-Sexto A, Gallego D, Leal F, Castejón-Fernández N, Navarrete R, Alcaide P, Couce ML, Martín-Hernández E, Quijada-Fraile P, Peña-Quintana L, Yahyaoui R, Correcher P, Ugarte M, Rodríguez-Pombo P, Pérez B. Identification of Clinical Variants beyond the Exome in Inborn Errors of Metabolism. Int J Mol Sci 2022; 23:ijms232112850. [PMID: 36361642 PMCID: PMC9654865 DOI: 10.3390/ijms232112850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 11/24/2022] Open
Abstract
Inborn errors of metabolism (IEM) constitute a huge group of rare diseases affecting 1 in every 1000 newborns. Next-generation sequencing has transformed the diagnosis of IEM, leading to its proposed use as a second-tier technology for confirming cases detected by clinical/biochemical studies or newborn screening. The diagnosis rate is, however, still not 100%. This paper reports the use of a personalized multi-omics (metabolomic, genomic and transcriptomic) pipeline plus functional genomics to aid in the genetic diagnosis of six unsolved cases, with a clinical and/or biochemical diagnosis of galactosemia, mucopolysaccharidosis type I (MPS I), maple syrup urine disease (MSUD), hyperphenylalaninemia (HPA), citrullinemia, or urea cycle deficiency. Eight novel variants in six genes were identified: six (four of them deep intronic) located in GALE, IDUA, PTS, ASS1 and OTC, all affecting the splicing process, and two located in the promoters of IDUA and PTS, thus affecting these genes’ expression. All the new variants were subjected to functional analysis to verify their pathogenic effects. This work underscores how the combination of different omics technologies and functional analysis can solve elusive cases in clinical practice.
Collapse
Affiliation(s)
- Alejandro Soriano-Sexto
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Diana Gallego
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Fátima Leal
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Natalia Castejón-Fernández
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Patricia Alcaide
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - María L. Couce
- Unit for the Diagnosis and Treatment of Congenital Metabolic Diseases, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, University of Santiago de Compostela, CIBERER, MetabERN, 15706 Santiago de Compostela, Spain
| | - Elena Martín-Hernández
- Unidad de Enfermedades Mitocondriales-Metabólicas Hereditarias, Servicio de Pediatría, Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) para Enfermedades Metabólicas Hereditarias, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Pilar Quijada-Fraile
- Unidad de Enfermedades Mitocondriales-Metabólicas Hereditarias, Servicio de Pediatría, Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) para Enfermedades Metabólicas Hereditarias, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Luis Peña-Quintana
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, Complejo Hospitalario Universitario Insular Materno-Infantil (CHUIMI), Universidad de Las Palmas de Gran Canaria, Asociación Canaria para La Investigación Pediátrica, Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBEROBN) ISCIII, 35016 Gran Canaria, Spain
| | - Raquel Yahyaoui
- Laboratory of Metabolic Disorders and Newborn Screening, Institute of Biomedical Research in Málaga (IBIMA-Plafatorma BIONAND), IBIMA-RARE, Málaga Regional University Hospital, 29010 Málaga, Spain
| | - Patricia Correcher
- Nutrition and Metabolophaties Unit, Hospital Universitario La Fe, 46026 Valencia, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Pilar Rodríguez-Pombo
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
- Correspondence:
| |
Collapse
|
9
|
Kido J, Sugawara K, Sawada T, Matsumoto S, Nakamura K. Pathogenic variants of ornithine transcarbamylase deficiency: Nation-wide study in Japan and literature review. Front Genet 2022; 13:952467. [PMID: 36303552 PMCID: PMC9593096 DOI: 10.3389/fgene.2022.952467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022] Open
Abstract
Ornithine transcarbamylase deficiency (OTCD) is an X-linked disorder. Several male patients with OTCD suffer from severe hyperammonemic crisis in the neonatal period, whereas others develop late-onset manifestations, including hyperammonemic coma. Females with heterozygous pathogenic variants in the OTC gene may develop a variety of clinical manifestations, ranging from asymptomatic conditions to severe hyperammonemic attacks, owing to skewed lyonization. We reported the variants of CPS1, ASS, ASL and OTC detected in the patients with urea cycle disorders through a nation-wide survey in Japan. In this study, we updated the variant data of OTC in Japanese patients and acquired information regarding genetic variants of OTC from patients with OTCD through an extensive literature review. The 523 variants included 386 substitution (330 missense, 53 nonsense, and 3 silent), eight deletion, two duplication, one deletion-insertion, 55 frame shift, two extension, and 69 no category (1 regulatory and 68 splice site error) mutations. We observed a genotype-phenotype relation between the onset time (neonatal onset or late onset), the severity, and genetic mutation in male OTCD patients because the level of deactivation of OTC significantly depends on the pathogenic OTC variants. In conclusion, genetic information about OTC may help to predict long-term outcomes and determine specific treatment strategies, such as liver transplantation, in patients with OTCD.
Collapse
Affiliation(s)
- Jun Kido
- Department of Pediatrics, Kumamoto University Hospital, Kumamoto, Japan
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Keishin Sugawara
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takaaki Sawada
- Department of Pediatrics, Kumamoto University Hospital, Kumamoto, Japan
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Shirou Matsumoto
- Department of Pediatrics, Kumamoto University Hospital, Kumamoto, Japan
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kimitoshi Nakamura
- Department of Pediatrics, Kumamoto University Hospital, Kumamoto, Japan
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| |
Collapse
|
10
|
Downes DJ, Hughes JR. Natural and Experimental Rewiring of Gene Regulatory Regions. Annu Rev Genomics Hum Genet 2022; 23:73-97. [PMID: 35472292 DOI: 10.1146/annurev-genom-112921-010715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The successful development and ongoing functioning of complex organisms depend on the faithful execution of the genetic code. A critical step in this process is the correct spatial and temporal expression of genes. The highly orchestrated transcription of genes is controlled primarily by cis-regulatory elements: promoters, enhancers, and insulators. The medical importance of this key biological process can be seen by the frequency with which mutations and inherited variants that alter cis-regulatory elements lead to monogenic and complex diseases and cancer. Here, we provide an overview of the methods available to characterize and perturb gene regulatory circuits. We then highlight mechanisms through which regulatory rewiring contributes to disease, and conclude with a perspective on how our understanding of gene regulation can be used to improve human health.
Collapse
Affiliation(s)
- Damien J Downes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom;
| |
Collapse
|
11
|
Feigenbaum A, Lamale-Smith L, Weinstein L. Considerations for prenatal and postpartum management of a female patient with ornithine transcarbamylase deficiency. Mol Genet Metab Rep 2022; 33:100894. [PMID: 36620386 PMCID: PMC9817480 DOI: 10.1016/j.ymgmr.2022.100894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 01/11/2023] Open
Abstract
We report on pregnancy management and outcomes in a 27-year-old female patient with ornithine transcarbamylase (OTC) deficiency, the most common inherited enzyme deficiency in the urea cycle. Our patient was diagnosed during childhood after hyperammonemia associated with surgery and steroid treatment and was well-controlled with nitrogen scavenger treatment, low-protein diet, and L-citrulline supplementation. OTC gene sequencing identified a variant of unknown significance that has more recently been classified as likely pathogenic. Women with OTC deficiency are at increased risk of hyperammonemia during pregnancy and the postpartum period, therefore monthly follow up and laboratory assessments are critical in management decision making. Our patient was maintained on glycerol phenylbutyrate, L-citrulline and essential amino acid supplements, along with restricted protein intake during pregnancy. A multidisciplinary approach with the obstetrics, prenatal genetics, high risk obstetric, and anesthesia teams was also necessary for optimal management during pregnancy, throughout labor and delivery, and during the postpartum period. After successful childbirth and discharge, our patient experienced a hyperammonemic crisis related to poor enteral nutrition, and acute management protocols were implemented to stabilize her. For her newborn son, acute hyperammonemia protocols were on standby, and newborn screening and laboratory testing were expedited to assess his risk. He was healthy and did not experience symptoms of concern. In this case report, we emphasize the importance of close collaboration with maternal-fetal medicine team members during and immediately after pregnancy to ensure successful management of a female patient with OTC deficiency and her newborn.
Collapse
Key Words
- BCAA, branched-chain amino acids
- BID, twice daily
- D10, 10% dextrose
- EAA, essential amino acids
- GPB, glycerol phenylbutyrate
- IV, intravenous
- NICU, neonatal intensive care unit
- OTC, ornithine transcarbamylase
- Ornithine transcarbamylase deficiency
- PICC, peripherally inserted central catheter
- PO, per os/orally
- Peripartum management
- Pregnancy
- TID, three times daily
- UCD, urea cycle disorder
- Urea cycle disorder
- X-linked, hyperammonemia
Collapse
Affiliation(s)
- Annette Feigenbaum
- Department of Pediatrics and Biochemical Genetics, Rady Children's Hospital-San Diego, University of California San Diego, 3020 Children's Way #5031, San Diego, CA 92123, USA
- Corresponding author at: 3020 Children's Way #5031, San Diego, CA 92123, USA.
| | - Leah Lamale-Smith
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, 9300 Campus Point Drive, #7433, San Diego, CA 92037, USA
| | - Lawrence Weinstein
- Department of Anesthesiology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| |
Collapse
|
12
|
Brown A, Mead ME, Steenwyk JL, Goldman GH, Rokas A. Extensive non-coding sequence divergence between the major human pathogen Aspergillus fumigatus and its relatives. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:802494. [PMID: 36866034 PMCID: PMC9977105 DOI: 10.3389/ffunb.2022.802494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/09/2022] [Indexed: 11/13/2022]
Abstract
Invasive aspergillosis is a deadly fungal disease; more than 400,000 patients are infected worldwide each year and the mortality rate can be as high as 50-95%. Of the ~450 species in the genus Aspergillus only a few are known to be clinically relevant, with the major pathogen Aspergillus fumigatus being responsible for ~50% of all invasive mold infections. Genomic comparisons between A. fumigatus and other Aspergillus species have historically focused on protein-coding regions. However, most A. fumigatus genes, including those that modulate its virulence, are also present in other pathogenic and non-pathogenic closely related species. Our hypothesis is that differential gene regulation - mediated through the non-coding regions upstream of genes' first codon - contributes to A. fumigatus pathogenicity. To begin testing this, we compared non-coding regions upstream of the first codon of single-copy orthologous genes from the two A. fumigatus reference strains Af293 and A1163 and eight closely related Aspergillus section Fumigati species. We found that these non-coding regions showed extensive sequence variation and lack of homology across species. By examining the evolutionary rates of both protein-coding and non-coding regions in a subset of orthologous genes with highly conserved non-coding regions across the phylogeny, we identified 418 genes, including 25 genes known to modulate A. fumigatus virulence, whose non-coding regions exhibit a different rate of evolution in A. fumigatus. Examination of sequence alignments of these non-coding regions revealed numerous instances of insertions, deletions, and other types of mutations of at least a few nucleotides in A. fumigatus compared to its close relatives. These results show that closely related Aspergillus species that vary greatly in their pathogenicity exhibit extensive non-coding sequence variation and identify numerous changes in non-coding regions of A. fumigatus genes known to contribute to virulence.
Collapse
Affiliation(s)
- Alec Brown
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Matthew E. Mead
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| |
Collapse
|
13
|
Knerr I, Cassiman D. Ornithine transcarbamylase deficiency: A diagnostic odyssey. J Inherit Metab Dis 2022; 45:661-662. [PMID: 35734906 PMCID: PMC9541173 DOI: 10.1002/jimd.12530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/22/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Ina Knerr
- National Centre for Inherited Metabolic DisordersChildren's Health Ireland (CHI) at Temple StreetDublinRepublic of Ireland
- University College Dublin (UCD)UCD School of MedicineDublinRepublic of Ireland
| | - David Cassiman
- Department of Gastroenterology‐Hepatology and Metabolic CenterUniversity Hospital LeuvenLeuvenBelgium
| |
Collapse
|
14
|
Han ST, Anderson KJ, Bjornsson HT, Longo N, Valle D. A promoter variant in the OTC gene associated with late and variable age of onset hyperammonemia. J Inherit Metab Dis 2022; 45:710-718. [PMID: 35605046 DOI: 10.1002/jimd.12524] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/12/2022] [Accepted: 05/20/2022] [Indexed: 11/11/2022]
Abstract
Ornithine transcarbamylase deficiency (OTCD) is an X-linked inborn error caused by loss of function variants in the OTC gene typically associated with severe neonatal hyperammonemia. Rare examples of late-onset OTCD have also been described. Here, we describe an OTC promoter variant, c.-106C>A, in a conserved HNF4a binding site, identified in two male siblings in Family 1 whose first and only recognized episodes of severe hyperammonemia occurred at ages 14 and 39 years, respectively. We identified the same OTC variant segregating in a large family with late-onset OTCD with variable expressivity (Family 2). We show that this OTC promoter variant reduces expression >5-fold in a dual-luciferase assay that tests promoter function. Addition of an upstream OTC enhancer increases expression of both the wild type and the c.-106C>A variant promoter constructs >5-fold with the mutant promoter still about fourfold lower than the wild type. Thus, in both contexts, the promoter variant results in substantially lower OTC expression. Under normal demand on urea cycle function, OTC expression in hemizygous males, although reduced, is sufficient to meet the demand for waste nitrogen excretion. However, in response to severe metabolic stress with attendant increased requirements on urea cycle function, the impaired promoter function results in inadequate OTC expression with resultant hyperammonemia. In the absence of precipitating events, hemizygotes with this allele are asymptomatic, explaining the late age of onset of hyperammonemia in affected individuals and the incomplete penetrance observed in some individuals in Family 2.
Collapse
Affiliation(s)
- Sangwoo T Han
- Predoctoral Training Program in Human Genetics, McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katherine J Anderson
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Hans T Bjornsson
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Landspitali University Hospital, Reykjavik, Iceland
| | - Nicola Longo
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - David Valle
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| |
Collapse
|
15
|
Steinhaus R, Robinson PN, Seelow D. FABIAN-variant: predicting the effects of DNA variants on transcription factor binding. Nucleic Acids Res 2022; 50:W322-W329. [PMID: 35639768 PMCID: PMC9252790 DOI: 10.1093/nar/gkac393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 12/03/2022] Open
Abstract
While great advances in predicting the effects of coding variants have been made, the assessment of non-coding variants remains challenging. This is especially problematic for variants within promoter regions which can lead to over-expression of a gene or reduce or even abolish its expression. The binding of transcription factors to the DNA can be predicted using position weight matrices (PWMs). More recently, transcription factor flexible models (TFFMs) have been introduced and shown to be more accurate than PWMs. TFFMs are based on hidden Markov models and can account for complex positional dependencies. Our new web-based application FABIAN-variant uses 1224 TFFMs and 3790 PWMs to predict whether and to which degree DNA variants affect the binding of 1387 different human transcription factors. For each variant and transcription factor, the software combines the results of different models for a final prediction of the resulting binding-affinity change. The software is written in C++ for speed but variants can be entered through a web interface. Alternatively, a VCF file can be uploaded to assess variants identified by high-throughput sequencing. The search can be restricted to variants in the vicinity of candidate genes. FABIAN-variant is available freely at https://www.genecascade.org/fabian/.
Collapse
Affiliation(s)
- Robin Steinhaus
- Exploratory Diagnostic Sciences, Berlin Institute of Health, 10117 Berlin, Germany.,Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06030, USA.,Institute for Systems Genomics, University of Connecticut, Farmington, CT 06030, USA
| | - Dominik Seelow
- Exploratory Diagnostic Sciences, Berlin Institute of Health, 10117 Berlin, Germany.,Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
| |
Collapse
|
16
|
Hertzog A, Selvanathan A, Halligan R, Fazio T, Jong G, Bratkovic D, Bhattacharya K, Tolun AA, Bennetts B, Fisk K. A serendipitous journey to a promoter variant: The c.‐
106C
>A variant and its role in late‐onset ornithine transcarbamylase deficiency. JIMD Rep 2022; 63:271-275. [PMID: 35822098 PMCID: PMC9259394 DOI: 10.1002/jmd2.12289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/15/2022] [Accepted: 04/01/2022] [Indexed: 11/19/2022] Open
Abstract
Ornithine transcarbamylase deficiency (OTCD) is an X‐linked urea cycle disorder characterised by reduced or absent OTC enzyme activity, resulting in the accumulation of neurotoxic ammonia. Approximately 80%–90% of the causative variants are identified by Sanger sequencing or multiplex ligation‐dependent probe amplification (MLPA) of the OTC gene. A 23‐year‐old male with biochemical evidence of OTCD was referred for molecular analysis. Initial Sanger sequencing yielded no pathogenic variants. MLPA testing raised suspicion of a mosaic deletion of exon 1; however, high‐resolution microarray did not identify a copy number variant on the X chromosome. Sequencing over the suspected breakpoint detected a hemizygous likely pathogenic promoter variant, c.‐106C > A, which was located within the MLPA probe binding site. Subsequently, historical patients referred to our centre, without a molecular aetiology for their OTCD, were re‐sequenced with these primers and this variant was also identified in two additional unrelated males. All three patients described in this case series have the late‐onset disease. Two presented at 5 years of age with vomiting, whilst the other was managed from birth based on a family history of late‐onset OTCD. One patient required liver transplantation due to recurrent decompensations; the other two are managed with a protein‐restricted diet. All three patients have not sustained any significant neurological insults and are functioning well as adults. These cases support screening of the promoter region within the OTC gene, particularly if a molecular basis has not been elucidated by MLPA or sequencing of the coding regions.
Collapse
Affiliation(s)
- Ashley Hertzog
- NSW Biochemical Genetics Service The Children's Hospital at Westmead Westmead New South Wales Australia
| | - Arthavan Selvanathan
- Genetic Metabolic Disorders Service The Children's Hospital at Westmead Westmead New South Wales Australia
| | - Rebecca Halligan
- Metabolic Unit Women's and Children's Hospital Adelaide South Australia Australia
| | - Timothy Fazio
- Metabolic Diseases Unit Royal Melbourne Hospital Parkville Victoria Australia
- Melbourne Medical School University of Melbourne Parkville Victoria Australia
| | - Gerard Jong
- Metabolic Diseases Unit Royal Melbourne Hospital Parkville Victoria Australia
- Melbourne Medical School University of Melbourne Parkville Victoria Australia
| | - Drago Bratkovic
- Metabolic Unit Women's and Children's Hospital Adelaide South Australia Australia
| | - Kaustuv Bhattacharya
- Genetic Metabolic Disorders Service The Children's Hospital at Westmead Westmead New South Wales Australia
- Disciplines of Genomic Medicine and Child and Adolescent Health Faculty of Medicine and Health, University of Sydney Sydney New South Wales Australia
| | - Adviye Ayper Tolun
- NSW Biochemical Genetics Service The Children's Hospital at Westmead Westmead New South Wales Australia
- Disciplines of Genomic Medicine and Child and Adolescent Health Faculty of Medicine and Health, University of Sydney Sydney New South Wales Australia
| | - Bruce Bennetts
- Disciplines of Genomic Medicine and Child and Adolescent Health Faculty of Medicine and Health, University of Sydney Sydney New South Wales Australia
- Department of Molecular Genetics Western Sydney Genetics Program, The Children's Hospital at Westmead Westmead New South Wales Australia
| | - Katrina Fisk
- Department of Molecular Genetics Western Sydney Genetics Program, The Children's Hospital at Westmead Westmead New South Wales Australia
| |
Collapse
|
17
|
Couchet M, Breuillard C, Corne C, Rendu J, Morio B, Schlattner U, Moinard C. Ornithine Transcarbamylase - From Structure to Metabolism: An Update. Front Physiol 2021; 12:748249. [PMID: 34658931 PMCID: PMC8517447 DOI: 10.3389/fphys.2021.748249] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/07/2021] [Indexed: 12/30/2022] Open
Abstract
Ornithine transcarbamylase (OTC; EC 2.1.3.3) is a ubiquitous enzyme found in almost all organisms, including vertebrates, microorganisms, and plants. Anabolic, mostly trimeric OTCs catalyze the production of L-citrulline from L-ornithine which is a part of the urea cycle. In eukaryotes, such OTC localizes to the mitochondrial matrix, partially bound to the mitochondrial inner membrane and part of channeling multi-enzyme assemblies. In mammals, mainly two organs express OTC: the liver, where it is an integral part of the urea cycle, and the intestine, where it synthesizes citrulline for export and plays a major role in amino acid homeostasis, particularly of L-glutamine and L-arginine. Here, we give an overview on OTC genes and proteins, their tissue distribution, regulation, and physiological function, emphasizing the importance of OTC and urea cycle enzymes for metabolic regulation in human health and disease. Finally, we summarize the current knowledge of OTC deficiency, a rare X-linked human genetic disorder, and its emerging role in various chronic pathologies.
Collapse
Affiliation(s)
- Morgane Couchet
- Université Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | - Charlotte Breuillard
- Université Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| | | | - John Rendu
- Centre Hospitalier Université Grenoble Alpes, Grenoble, France
| | - Béatrice Morio
- CarMeN Laboratory, INSERM U1060, INRAE U1397, Lyon, France
| | - Uwe Schlattner
- Université Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France.,Institut Universitaire de France, Paris, France
| | - Christophe Moinard
- Université Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France
| |
Collapse
|
18
|
Pribožič L, Žerjav Tanšek M, Herga P, Osredkar D, Rajtar Osredkar S, Vidmar I, Repič Lampret B, Klemenčič S, Bratina N, Battelino T, Groselj U. Reye Syndrome with Severe Hyperammonemia and a Good Neurological Outcome. AMERICAN JOURNAL OF CASE REPORTS 2021; 22:e932864. [PMID: 34629460 PMCID: PMC8522526 DOI: 10.12659/ajcr.932864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Patient: Male, 4-year-old
Final Diagnosis: Reye syndrome
Symptoms: Hypoglycemia • disturbance of consciousness • diarrhoea • signs of respiratory infection • vomiting and nausea
Medication: —
Clinical Procedure: —
Specialty: Critical Care Medicine • Endocrinology and Metabolic • Pediatrics and Neonatology
Collapse
Affiliation(s)
- Lucija Pribožič
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children's Hospital, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Mojca Žerjav Tanšek
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children's Hospital, University Medical Center Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Primož Herga
- Department of Pediatric Surgery and Intensive Care, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Damjan Osredkar
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.,Department for Pediatric Neurology, University Children's Hospital, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Simona Rajtar Osredkar
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children's Hospital, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Ivan Vidmar
- Department of Pediatric Surgery and Intensive Care, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Barbka Repič Lampret
- Clinical Institute for Special Laboratory Diagnostics, University Children's Hospital, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Simona Klemenčič
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children's Hospital, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Nataša Bratina
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children's Hospital, University Medical Center Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Tadej Battelino
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children's Hospital, University Medical Center Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Urh Groselj
- Department of Pediatric Endocrinology, Diabetes and Metabolic Diseases, University Children's Hospital, University Medical Center Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
19
|
Gobin-Limballe S, Ottolenghi C, Reyal F, Arnoux JB, Magen M, Simon M, Brassier A, Jabot-Hanin F, Lonlay PD, Pontoizeau C, Guirat M, Rio M, Gesny R, Gigarel N, Royer G, Steffann J, Munnich A, Bonnefont JP. OTC deficiency in females: Phenotype-genotype correlation based on a 130-family cohort. J Inherit Metab Dis 2021; 44:1235-1247. [PMID: 34014569 DOI: 10.1002/jimd.12404] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/30/2022]
Abstract
OTC deficiency, an inherited urea cycle disorder, is caused by mutations in the X-linked OTC gene. Phenotype-genotype correlations are well understood in males but still poorly known in females. Taking advantage of a cohort of 130 families (289 females), we assessed the relative contribution of OTC enzyme activity, X chromosome inactivation, and OTC gene sequencing to genetic counseling in heterozygous females. Twenty two percent of the heterozygous females were clinically affected, with episodic (11%), chronic (7.5%), or neonatal forms of the disease (3.5%). Overall mortality rate was 4%. OTC activity, ranging from 0% to 60%, did not correlate with phenotype at the individual level. Analysis of multiple samples from 4 mutant livers showed intra-hepatic variability of OTC activity and X inactivation profile (range of variability: 30% and 20%, respectively) without correlation between both parameters for 3 of the 4 livers. Ninety disease-causing variants were found, 27 of which were novel. Mutations were classified as "mild" or "severe," based on male phenotypes and/or in silico prediction. In our cohort, a serious disease occurred in 32% of females with a severe mutation, compared to 4% in females with a mild mutation (odds ratio = 1.365; P = 1.6e-06). These data should help prenatal diagnosis for heterozygous females and genetic counseling after fortuitous findings of OTC variants in pangenomic sequencing.
Collapse
Affiliation(s)
| | - Chris Ottolenghi
- Metabolomic and Proteomic Biochemistry Department, Necker Hospital, APHP Centre- Paris University, Paris, France
- INSERM UMR1163, Institut Imagine, Paris University, Paris, France
| | - Fabien Reyal
- Molecular Genetics Department, Necker Hospital, APHP Centre-Paris University, Paris, France
- Breast Gynecologic Cancer Reconstructive Team, Institut Curie, Paris University, Paris, France
| | - Jean-Baptiste Arnoux
- Inherited Metabolic Disease Department and National Reference Centre for Inherited Metabolic diseases, Necker Hospital, APHP Centre-Paris University, Paris, France
- INSERM U1151, INEM, Paris University, Paris, France
| | - Maryse Magen
- Molecular Genetics Department, Necker Hospital, APHP Centre-Paris University, Paris, France
| | - Marie Simon
- Molecular Genetics Department, Necker Hospital, APHP Centre-Paris University, Paris, France
| | - Anaïs Brassier
- Inherited Metabolic Disease Department and National Reference Centre for Inherited Metabolic diseases, Necker Hospital, APHP Centre-Paris University, Paris, France
- INSERM U1151, INEM, Paris University, Paris, France
| | - Fabienne Jabot-Hanin
- Bioinformatics Platform, Paris University, INSERM UMR1163, Institut Imagine, Paris, France
- Structure Federative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Pascale De Lonlay
- Inherited Metabolic Disease Department and National Reference Centre for Inherited Metabolic diseases, Necker Hospital, APHP Centre-Paris University, Paris, France
- INSERM U1151, INEM, Paris University, Paris, France
| | - Clement Pontoizeau
- Metabolomic and Proteomic Biochemistry Department, Necker Hospital, APHP Centre- Paris University, Paris, France
- INSERM UMR1163, Institut Imagine, Paris University, Paris, France
| | - Manel Guirat
- Molecular Genetics Department, Necker Hospital, APHP Centre-Paris University, Paris, France
| | - Marlene Rio
- Clinical Genetics Department, Necker Hospital, APHP Centre-Paris University, Paris, France
| | - Roselyne Gesny
- Molecular Genetics Department, Necker Hospital, APHP Centre-Paris University, Paris, France
| | - Nadine Gigarel
- Molecular Genetics Department, Necker Hospital, APHP Centre-Paris University, Paris, France
| | - Ghislaine Royer
- Molecular Genetics Department, Necker Hospital, APHP Centre-Paris University, Paris, France
| | - Julie Steffann
- Molecular Genetics Department, Necker Hospital, APHP Centre-Paris University, Paris, France
- INSERM UMR1163, Institut Imagine, Paris University, Paris, France
| | - Arnold Munnich
- INSERM UMR1163, Institut Imagine, Paris University, Paris, France
- Clinical Genetics Department, Necker Hospital, APHP Centre-Paris University, Paris, France
| | - Jean-Paul Bonnefont
- Molecular Genetics Department, Necker Hospital, APHP Centre-Paris University, Paris, France
- INSERM UMR1163, Institut Imagine, Paris University, Paris, France
| |
Collapse
|
20
|
Lopes‐Marques M, Pacheco AR, Peixoto MJ, Cardoso AR, Serrano C, Amorim A, Prata MJ, Cooper DN, Azevedo L. Common polymorphic OTC variants can act as genetic modifiers of enzymatic activity. Hum Mutat 2021; 42:978-989. [PMID: 34015158 PMCID: PMC8362079 DOI: 10.1002/humu.24221] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 05/05/2021] [Accepted: 05/18/2021] [Indexed: 12/24/2022]
Abstract
Understanding the role of common polymorphisms in modulating the clinical phenotype when they co‐occur with a disease‐causing lesion is of critical importance in medical genetics. We explored the impact of apparently neutral common polymorphisms, using the gene encoding the urea cycle enzyme, ornithine transcarbamylase (OTC), as a model system. Distinct combinations of genetic backgrounds embracing two missense polymorphisms were created in cis with the pathogenic p.Arg40His replacement. In vitro enzymatic assays revealed that the polymorphic variants were able to modulate OTC activity both in the presence or absence of the pathogenic lesion. First, we found that the combination of the minor alleles of polymorphisms p.Lys46Arg and p.Gln270Arg significantly enhanced enzymatic activity in the wild‐type protein. Second, enzymatic assays revealed that the minor allele of the p.Gln270Arg polymorphism was capable of ameliorating OTC activity when combined in cis with the pathogenic p.Arg40His replacement. Structural analysis predicted that the minor allele of the p.Gln270Arg polymorphism would serve to stabilize the OTC wild‐type protein, thereby corroborating the results of the experimental assays. Our findings demonstrate the potential importance of cis‐interactions between common polymorphic variants and pathogenic missense mutations and illustrate how standing genetic variation can modulate protein function.
Collapse
Affiliation(s)
- Mónica Lopes‐Marques
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - Ana Rita Pacheco
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
| | - Maria João Peixoto
- ICVS‐ Life and Health Sciences Research Institute, School of MedicineUniversity of MinhoBragaPortugal
- ICVS/3B's‐PT Government Associate LaboratoryBragaGuimarãesPortugal
| | - Ana Rita Cardoso
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - Catarina Serrano
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - António Amorim
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - Maria João Prata
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| | - David N. Cooper
- Institute of Medical Genetics; School of MedicineCardiff UniversityCardiffUK
| | - Luísa Azevedo
- i3S‐Instituto de Investigação e Inovação em Saúde, Population Genetics and Evolution GroupUniversidade do PortoPortoPortugal
- IPATIMUP‐Institute of Molecular Pathology and Immunology, Population Genetics and Evolution GroupUniversity of PortoPortoPortugal
- Faculty of Sciences, Department of BiologyUniversity of PortoPortoPortugal
| |
Collapse
|
21
|
Roos D, de Boer M. Mutations in cis that affect mRNA synthesis, processing and translation. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166166. [PMID: 33971252 DOI: 10.1016/j.bbadis.2021.166166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022]
Abstract
Genetic mutations that cause hereditary diseases usually affect the composition of the transcribed mRNA and its encoded protein, leading to instability of the mRNA and/or the protein. Sometimes, however, such mutations affect the synthesis, the processing or the translation of the mRNA, with similar disastrous effects. We here present an overview of mRNA synthesis, its posttranscriptional modification and its translation into protein. We then indicate which elements in these processes are known to be affected by pathogenic mutations, but we restrict our review to mutations in cis, in the DNA of the gene that encodes the affected protein. These mutations can be in enhancer or promoter regions of the gene, which act as binding sites for transcription factors involved in pre-mRNA synthesis. We also describe mutations in polyadenylation sequences and in splice site regions, exonic and intronic, involved in intron removal. Finally, we include mutations in the Kozak sequence in mRNA, which is involved in protein synthesis. We provide examples of genetic diseases caused by mutations in these DNA regions and refer to databases to help identify these regions. The over-all knowledge of mRNA synthesis, processing and translation is essential for improvement of the diagnosis of patients with genetic diseases.
Collapse
Affiliation(s)
- Dirk Roos
- Sanquin Blood Supply Organization, Dept. of Blood Cell Research, Landsteiner Laboratory, Amsterdam University Medical Centre, location AMC, University of Amsterdam, Amsterdam, the Netherlands.
| | - Martin de Boer
- Sanquin Blood Supply Organization, Dept. of Blood Cell Research, Landsteiner Laboratory, Amsterdam University Medical Centre, location AMC, University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
22
|
Kumar RD, Burrage LC, Bartos J, Ali S, Schmitt E, Nagamani SCS, LeMons C. A deep intronic variant is a common cause of OTC deficiency in individuals with previously negative genetic testing. Mol Genet Metab Rep 2021; 26:100706. [PMID: 33489762 PMCID: PMC7809430 DOI: 10.1016/j.ymgmr.2020.100706] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 12/28/2020] [Indexed: 12/31/2022] Open
Abstract
Pathogenic variants in non-coding regions of genes encoding enzymes or transporters of the urea cycle can lead to urea cycle disorders (UCDs). However, not all commercially available testing platforms interrogate these regions. Here, we used a gene panel based on massively parallel sequencing (MPS) in 10 individuals with clinical or pedigree-based evidence of a proximal UCD but without a molecular confirmation of the diagnosis. We identified causal variant(s) in 5 of 10 individuals, including in 3 of 7 individuals in whom prior molecular testing was unrevealing. We show that a deep-intronic pathogenic variant in OTC, c.540+265G>A, is an important cause of ornithine transcarbamylase (OTC) deficiency.
Collapse
Affiliation(s)
- Runjun D Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Jan Bartos
- National Urea Cycle Disorders Foundation, Pasadena, CA, USA
| | - Saima Ali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Texas Children's Hospital, Houston, TX, USA
| | - Cynthia LeMons
- National Urea Cycle Disorders Foundation, Pasadena, CA, USA
| |
Collapse
|
23
|
Makris G, Lauber M, Rüfenacht V, Gemperle C, Diez-Fernandez C, Caldovic L, Froese DS, Häberle J. Clinical and structural insights into potential dominant negative triggers of proximal urea cycle disorders. Biochimie 2020; 183:89-99. [PMID: 33309754 DOI: 10.1016/j.biochi.2020.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/31/2022]
Abstract
Despite biochemical and genetic testing being the golden standards for identification of proximal urea cycle disorders (UCDs), genotype-phenotype correlations are often unclear. Co-occurring partial defects affecting more than one gene have not been demonstrated so far in proximal UCDs. Here, we analyzed the mutational spectrum of 557 suspected proximal UCD individuals. We probed oligomerizing forms of NAGS, CPS1 and OTC, and evaluated the surface exposure of residues mutated in heterozygously affected individuals. BN-PAGE and gel-filtration chromatography were employed to discover protein-protein interactions within recombinant enzymes. From a total of 281 confirmed patients, only 15 were identified as "heterozygous-only" candidates (i.e. single defective allele). Within these cases, the only missense variants to potentially qualify as dominant negative triggers were CPS1 p.Gly401Arg and NAGS p.Thr181Ala and p.Tyr512Cys, as assessed by residue oligomerization capacity and surface exposure. However, all three candidates seem to participate in critical intramolecular functions, thus, unlikely to facilitate protein-protein interactions. This interpretation is further supported by BN-PAGE and gel-filtration analyses revealing no multiprotein proximal urea cycle complex formation. Collectively, genetic analysis, structural considerations and in vitro experiments point against a prominent role of dominant negative effects in human proximal UCDs.
Collapse
Affiliation(s)
- Georgios Makris
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Matthias Lauber
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Véronique Rüfenacht
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Corinne Gemperle
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Carmen Diez-Fernandez
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland; Nextech Invest, Bahnhofstrasse 18, 8001, Zurich, Switzerland
| | - Ljubica Caldovic
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Johannes Häberle
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland.
| |
Collapse
|
24
|
Cirulli ET, White S, Read RW, Elhanan G, Metcalf WJ, Tanudjaja F, Fath DM, Sandoval E, Isaksson M, Schlauch KA, Grzymski JJ, Lu JT, Washington NL. Genome-wide rare variant analysis for thousands of phenotypes in over 70,000 exomes from two cohorts. Nat Commun 2020; 11:542. [PMID: 31992710 PMCID: PMC6987107 DOI: 10.1038/s41467-020-14288-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/19/2019] [Indexed: 02/08/2023] Open
Abstract
Understanding the impact of rare variants is essential to understanding human health. We analyze rare (MAF < 0.1%) variants against 4264 phenotypes in 49,960 exome-sequenced individuals from the UK Biobank and 1934 phenotypes (1821 overlapping with UK Biobank) in 21,866 members of the Healthy Nevada Project (HNP) cohort who underwent Exome + sequencing at Helix. After using our rare-variant-tailored methodology to reduce test statistic inflation, we identify 64 statistically significant gene-based associations in our meta-analysis of the two cohorts and 37 for phenotypes available in only one cohort. Singletons make significant contributions to our results, and the vast majority of the associations could not have been identified with a genotyping chip. Our results are available for interactive browsing in a webapp (https://ukb.research.helix.com). This comprehensive analysis illustrates the biological value of large, deeply phenotyped cohorts of unselected populations coupled with NGS data. Population-based association analyses of rare genetic variants with complex traits are limited by the availability of data from sufficiently large cohorts. Here, Cirulli et al. report gene-based collapsing analysis of exomes from 49,960 participants of the UK Biobank and 21,866 participants of the Healthy Nevada Project over a total of 4377 traits.
Collapse
Affiliation(s)
| | - Simon White
- Helix, 101S Ellsworth Ave Suite 350, San Mateo, CA, 94401, USA
| | - Robert W Read
- Desert Research Institute, 2215 Raggio Pkwy, Reno, NV, 89512, USA.,Renown Institute of Health Innovation, Reno, NV, 89512, USA
| | - Gai Elhanan
- Desert Research Institute, 2215 Raggio Pkwy, Reno, NV, 89512, USA.,Renown Institute of Health Innovation, Reno, NV, 89512, USA
| | - William J Metcalf
- Desert Research Institute, 2215 Raggio Pkwy, Reno, NV, 89512, USA.,Renown Institute of Health Innovation, Reno, NV, 89512, USA
| | | | - Donna M Fath
- Helix, 101S Ellsworth Ave Suite 350, San Mateo, CA, 94401, USA
| | - Efren Sandoval
- Helix, 101S Ellsworth Ave Suite 350, San Mateo, CA, 94401, USA
| | - Magnus Isaksson
- Helix, 101S Ellsworth Ave Suite 350, San Mateo, CA, 94401, USA
| | - Karen A Schlauch
- Desert Research Institute, 2215 Raggio Pkwy, Reno, NV, 89512, USA.,Renown Institute of Health Innovation, Reno, NV, 89512, USA
| | - Joseph J Grzymski
- Desert Research Institute, 2215 Raggio Pkwy, Reno, NV, 89512, USA.,Renown Institute of Health Innovation, Reno, NV, 89512, USA
| | - James T Lu
- Helix, 101S Ellsworth Ave Suite 350, San Mateo, CA, 94401, USA
| | | |
Collapse
|
25
|
Rowlands CF, Baralle D, Ellingford JM. Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing. Cells 2019; 8:E1513. [PMID: 31779139 PMCID: PMC6953098 DOI: 10.3390/cells8121513] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 12/13/2022] Open
Abstract
Defects in pre-mRNA splicing are frequently a cause of Mendelian disease. Despite the advent of next-generation sequencing, allowing a deeper insight into a patient's variant landscape, the ability to characterize variants causing splicing defects has not progressed with the same speed. To address this, recent years have seen a sharp spike in the number of splice prediction tools leveraging machine learning approaches, leaving clinical geneticists with a plethora of choices for in silico analysis. In this review, some basic principles of machine learning are introduced in the context of genomics and splicing analysis. A critical comparative approach is then used to describe seven recent machine learning-based splice prediction tools, revealing highly diverse approaches and common caveats. We find that, although great progress has been made in producing specific and sensitive tools, there is still much scope for personalized approaches to prediction of variant impact on splicing. Such approaches may increase diagnostic yields and underpin improvements to patient care.
Collapse
Affiliation(s)
- Charlie F Rowlands
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WJ, UK;
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PR, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, MP808, Tremona Road, Southampton SO16 6YD, UK
| | - Jamie M Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WJ, UK;
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PR, UK
| |
Collapse
|
26
|
Untargeted metabolomic profiling reveals multiple pathway perturbations and new clinical biomarkers in urea cycle disorders. Genet Med 2019; 21:1977-1986. [PMID: 30670878 PMCID: PMC6650380 DOI: 10.1038/s41436-019-0442-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/09/2019] [Indexed: 12/30/2022] Open
Abstract
Purpose: Untargeted metabolomic analysis is increasingly being used in the screening and management of individuals with inborn errors of metabolism (IEM). We aimed to test whether untargeted metabolomic analysis in plasma might be useful for monitoring the disease course and management of urea cycle disorders (UCDs). Methods: Untargeted mass spectrometry-based metabolomic analysis was used to generate z-scores for more than 900 metabolites in plasma from 48 individuals with various UCDs. Pathway analysis was used to identify common pathways that were perturbed in each UCD. Results: Our metabolomic analysis in plasma identified multiple potentially neurotoxic metabolites of arginine in arginase deficiency and, thus, may have utility in monitoring the efficacy of treatment in arginase deficiency. In addition, we were also able to detect multiple biochemical perturbations in all UCDs that likely reflect clinical management, including metabolite alterations secondary to dietary and medication management. Conclusions: In addition to utility in screening for IEM, our results suggest that untargeted metabolomic analysis in plasma may be beneficial for monitoring efficacy of clinical management and off-target effects of medications in UCDs and potentially other IEM.
Collapse
|
27
|
Yokoi K, Nakajima Y, Inagaki H, Tsutsumi M, Ito T, Kurahashi H. Exonic duplication of the OTC gene by a complex rearrangement that likely occurred via a replication-based mechanism: a case report. BMC MEDICAL GENETICS 2018; 19:210. [PMID: 30541480 PMCID: PMC6292170 DOI: 10.1186/s12881-018-0733-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/03/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND Ornithine transcarbamylase deficiency (OTCD) is an X-linked recessive disorder involving a defect in the urea cycle caused by OTC gene mutations. Although a total of 417 disease-causing mutations in OTC have been reported, structural abnormalities in this gene are rare. We here describe a female OTCD case caused by an exonic duplication of the OTC gene (exons 1-6). CASE PRESENTATION A 23-year-old woman with late-onset OTCD diagnosed by biochemical testing was subjected to subsequent genetic testing. Sanger sequencing revealed no pathogenic mutation throughout the coding exons of the OTC gene, but multiplex ligation-dependent probe amplification (MLPA) revealed duplication of exons 1-6. Further genetic analyses revealed an inversion of duplicated exon 1 and a tandem duplication of exons 2-6. Each of the junctions of the inversion harbored a microhomology and non-templated microinsertion, respectively, suggesting a replication-based mechanism. The duplication was also of de novo origin but segregation analysis indicated that it took place in the paternal chromosome. CONCLUSION We report the first OTCD case harboring an exonic duplication in the OTC gene. The functional defects caused by this anomaly were determined via structural analysis of its complex rearrangements.
Collapse
Affiliation(s)
- Katsuyuki Yokoi
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan.,Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Yoko Nakajima
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Makiko Tsutsumi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Tetsuya Ito
- Department of Pediatrics, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan.
| |
Collapse
|
28
|
Li S, Cai Y, Shi C, Liu M, Liu B, Lin L, Xiao X, Hao H. Gene Mutation Analysis and Prenatal Diagnosis of the Ornithine Transcarbamylase (OTC) Gene in Two Families with Ornithine Transcarbamylase Deficiency. Med Sci Monit 2018; 24:7431-7437. [PMID: 30333473 PMCID: PMC6354644 DOI: 10.12659/msm.911295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background The aim of this study was to perform gene detection in 2 clinical cases of highly suspected ornithine transcarbamylase deficiency (OTCD) pediatric patients by first-generation sequencing technology in order to confirm the pathogenic genetic factors of their families and allow the families to undergo genetic counselling and prenatal diagnosis. Material/Methods The peripheral DNA samples of 2 children with highly suspected OTCD (the probands) and their parents were collected. DNA fragments corresponding to exons 1–10 of the OTC gene from the samples were amplified using polymerase chain reaction (PCR), and then subjected to Sanger sequencing to confirm the pathogenic mutation sites. Results The probands were both confirmed to have OTCD. The proband in Family 1 was a male carrying a c.867+1G>C mutation at a splice site within the OTC gene. The gene detection results of amniotic fluid cells at 16 weeks of pregnancy showed that the fetus was a male who also carried the c.867+1G>C mutation. The proband in Family 2 was a male carrying a c.782T>C(p. I261T) mutation in the OTC gene. The gene detection results of amniotic fluid cells at 18 weeks showed that the fetus was a male without pathogenic mutations in the OTC gene. The gene detection results of peripheral blood from the fetus after birth were consistent with those obtained from amniotic fluid cells. Conclusions Pediatric children who are clinically suspected of OTCD can receive a definitive diagnosis through OTC gene detection.
Collapse
Affiliation(s)
- Sitao Li
- Department of Neonatology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China (mainland)
| | - Yao Cai
- Department of Neonatology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China (mainland)
| | - Congcong Shi
- Department of Neonatology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China (mainland)
| | - Mengxian Liu
- Department of Neonatology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China (mainland)
| | - Bingqing Liu
- Department of Neonatology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China (mainland)
| | - Lin Lin
- Department of Obstetrics and Gynecology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China (mainland)
| | - Xin Xiao
- Department of Neonatology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China (mainland)
| | - Hu Hao
- Department of Neonatology, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China (mainland)
| |
Collapse
|