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Ilic N, Krasic S, Maric N, Gasic V, Krstic J, Cvetkovic D, Miljkovic V, Zec B, Maver A, Vukomanovic V, Sarajlija A. Noonan Syndrome: Relation of Genotype to Cardiovascular Phenotype-A Multi-Center Retrospective Study. Genes (Basel) 2024; 15:1463. [PMID: 39596663 PMCID: PMC11594011 DOI: 10.3390/genes15111463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 11/09/2024] [Accepted: 11/10/2024] [Indexed: 11/29/2024] Open
Abstract
Background: Noonan syndrome (NS) is a congenital genetic disorder with a prevalence of 1 in 1000 to 2500 live births, and is characterized by distinctive facial features, short stature, chest deformities, and congenital heart disease. This study aims to evaluate the prevalence of specific genetic mutations and their impact on cardiovascular and other outcomes in NS. Methods: We conducted a retrospective clinical study of 25 pediatric patients diagnosed with NS at two institutions: The Mother and Child Health Care Institute of Serbia and the Clinic for Children Diseases, University Clinical Center of the Republic of Srpska. Patients underwent whole-exome sequencing (WES) to identify genetic mutations. Clinical data, including cardiovascular manifestations, psychomotor development, and stature, were analyzed in relation to mutation types. Results: The cohort comprised 60% male and 40% female patients, with a median age at diagnosis of 7.2 years. Cardiovascular abnormalities were present in 88% of patients. Mutations in PTPN11 were most commonly associated with pulmonary valve stenosis (PVS), while RAF1 mutations were prevalent in patients with hypertrophic cardiomyopathy (HCM). No significant association was found between cardiac disease and delayed psychomotor development (p = 0.755), even though the likelihood ratio showed significance in that regard (p = 0.018). Short stature was observed in 48% of patients but was not significantly correlated with genetic type of disease, presence of cardiac disease, or developmental delay. Conclusions: The study confirms the high prevalence of cardiovascular manifestations in NS and highlights genotype-phenotype correlations. While cardiac abnormalities are common, their impact on psychomotor development and stature is less clear. Further research is needed to explore genetic interactions influencing these outcomes and refine clinical management strategies.
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Affiliation(s)
- Nikola Ilic
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.K.)
| | - Stasa Krasic
- Department of Cardiology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (S.K.); (V.V.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Nina Maric
- Clinic for Children’s Disease, University Clinical Center of the Republic of Srpska, 78000 Banja Luka, Bosnia and Herzegovina;
| | - Vladimir Gasic
- Laboratory for Molecular Biomedicine, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia;
| | - Jovana Krstic
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.K.)
| | - Dimitrije Cvetkovic
- Department of Endocrinology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia;
| | - Vesna Miljkovic
- Department of Endocrinology, University Clinical Center of the Republic of Srpska, 78000 Banja Luka, Bosnia and Herzegovina;
| | - Boris Zec
- Department of Cardiology, University Clinical Center of the Republic of Srpska, 78000 Banja Luka, Bosnia and Herzegovina;
| | - Ales Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia;
| | - Vladislav Vukomanovic
- Department of Cardiology, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (S.K.); (V.V.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Adrijan Sarajlija
- Clinical Genetics Outpatient Clinic, Mother and Child Health Care Institute of Serbia “Dr Vukan Cupic”, 11070 Belgrade, Serbia; (N.I.); (J.K.)
- Department of Pediatrics, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia
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Torreggiani S, Castellan FS, Aksentijevich I, Beck DB. Somatic mutations in autoinflammatory and autoimmune disease. Nat Rev Rheumatol 2024; 20:683-698. [PMID: 39394526 DOI: 10.1038/s41584-024-01168-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2024] [Indexed: 10/13/2024]
Abstract
Somatic mutations (also known as acquired mutations) are emerging as common, age-related processes that occur in all cells throughout the body. Somatic mutations are canonically linked to malignant processes but over the past decade have been increasingly causally connected to benign diseases including rheumatic conditions. Here we outline the contribution of somatic mutations to complex and monogenic immunological diseases with a detailed review of unique aspects associated with such causes. Somatic mutations can cause early- or late-onset rheumatic monogenic diseases but also contribute to the pathogenesis of complex inflammatory and immune-mediated diseases, affect disease progression and define new clinical subtypes. Although even variants with a low variant allele fraction can be pathogenic, clonal dynamics could lead to changes over time in the proportion of mutant cells, with possible phenotypic consequences for the individual. Thus, somatic mutagenesis and clonal expansion have relevant implications in genetic testing and counselling. On the basis of both increased recognition of somatic diseases in clinical practice and improved technical and bioinformatic processes, we hypothesize that there will be an ever-expanding list of somatic mutations in various genes leading to inflammatory conditions, particularly in late-onset disease.
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Affiliation(s)
- Sofia Torreggiani
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
- Epidemiology and Human Genetics, Graduate Program in Life Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Flore S Castellan
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David B Beck
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY, USA.
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3
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Nakamura A, Nomura S, Hara S, Thamamongood T, Maehara T, Nariai T, Khairullah S, Tan KS, Azuma K, Chida-Nagai A, Furutani Y, Hori T, Yamaguchi K, Kawamata T, Roder C, Akagawa H. Whole-exome sequencing reveals the genetic causes and modifiers of moyamoya syndrome. Sci Rep 2024; 14:22720. [PMID: 39367156 PMCID: PMC11452616 DOI: 10.1038/s41598-024-72043-5] [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: 10/09/2023] [Accepted: 09/03/2024] [Indexed: 10/06/2024] Open
Abstract
Moyamoya vasculopathy secondary to various genetic disorders is classified as moyamoya syndrome (MMS). Recent studies indicate MMS occurs due to a combination of genetic modifiers and causative mutations for the primary genetic disorders. We performed whole-exome sequencing (WES) in 13 patients with various genetic disorders who developed MMS. WES successfully revealed the genetic diagnoses of neurofibromatosis type 1 (NF-1), Down syndrome, multisystemic smooth muscle dysfunction syndrome, Noonan syndrome, and alpha thalassemia. The previously reported modifier genes, RNF213 and MRVI1, were confirmed in the NF-1 and Down syndrome cases. Further analysis revealed rare hypomorphic variants in the causative genes of the primary disorders underlying MMS, such as Alagille syndrome and Rasopathies, conferred susceptibility to MMS. Genes involved in the development of pulmonary arterial hypertension (PAH), such as ABCC8 and BMPR2, were also identified as potential modifiers. The rare variants in the MMS and PAH genes were significantly enriched in the eight Japanese patients with MMS compared with the 104 Japanese individuals from the 1000 Genomes Project. Disease genes associated with the arterial occlusive conditions represented by those of Rasopathies and PAH may provide novel diagnostic markers and future therapeutic targets for MMS as well as moyamoya disease with an unknown cause.
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Affiliation(s)
- Akikazu Nakamura
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Shunsuke Nomura
- Department of Neurosurgery, Tokyo Women's Medical University Yachiyo Medical Center, Chiba, Japan
- Krembil Brain Institute, University Health Network, University of Toronto, Toronto, Canada
| | - Shoko Hara
- Department of Neurosurgery, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Taketoshi Maehara
- Department of Neurosurgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tadashi Nariai
- Department of Neurosurgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shasha Khairullah
- Haematology Unit, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kay Sin Tan
- Division of Neurology, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kenko Azuma
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Ayako Chida-Nagai
- Department of Pediatrics, Hokkaido University Hospital, Sapporo, Japan
- Department of Pediatric Cardiology and Adult Congenital Cardiology, Tokyo Women's Medical University, Tokyo, Japan
| | - Yoshiyuki Furutani
- Department of Pediatric Cardiology and Adult Congenital Cardiology, Tokyo Women's Medical University, Tokyo, Japan
| | - Takahiro Hori
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Koji Yamaguchi
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Takakazu Kawamata
- Department of Neurosurgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Constantin Roder
- Department of Neurosurgery, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Hiroyuki Akagawa
- Institute for Comprehensive Medical Sciences, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan.
- Department of Neurosurgery, Tokyo Women's Medical University Adachi Medical Center, Tokyo, Japan.
- Medical AI Center, Tokyo Women's Medical University, Tokyo, Japan.
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4
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Ham H, Jing H, Lamborn IT, Kober MM, Koval A, Berchiche YA, Anderson DE, Druey KM, Mandl JN, Isidor B, Ferreira CR, Freeman AF, Ganesan S, Karsak M, Mustillo PJ, Teo J, Zolkipli-Cunningham Z, Chatron N, Lecoquierre F, Oler AJ, Schmid JP, Kuhns DB, Xu X, Hauck F, Al-Herz W, Wagner M, Terhal PA, Muurinen M, Barlogis V, Cruz P, Danielson J, Stewart H, Loid P, Rading S, Keren B, Pfundt R, Zarember KA, Vill K, Potocki L, Olivier KN, Lesca G, Faivre L, Wong M, Puel A, Chou J, Tusseau M, Moutsopoulos NM, Matthews HF, Simons C, Taft RJ, Soldatos A, Masle-Farquhar E, Pittaluga S, Brink R, Fink DL, Kong HH, Kabat J, Kim WS, Bierhals T, Meguro K, Hsu AP, Gu J, Stoddard J, Banos-Pinero B, Slack M, Trivellin G, Mazel B, Soomann M, Li S, Watts VJ, Stratakis CA, Rodriguez-Quevedo MF, Bruel AL, Lipsanen-Nyman M, Saultier P, Jain R, Lehalle D, Torres D, Sullivan KE, Barbarot S, Neu A, Duffourd Y, Similuk M, McWalter K, Blanc P, Bézieau S, Jin T, Geha RS, Casanova JL, Makitie OM, Kubisch C, Edery P, Christodoulou J, Germain RN, Goodnow CC, Sakmar TP, Billadeau DD, Küry S, Katanaev VL, Zhang Y, Lenardo MJ, Su HC. Germline mutations in a G protein identify signaling cross-talk in T cells. Science 2024; 385:eadd8947. [PMID: 39298586 DOI: 10.1126/science.add8947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/15/2023] [Accepted: 07/12/2024] [Indexed: 09/22/2024]
Abstract
Humans with monogenic inborn errors responsible for extreme disease phenotypes can reveal essential physiological pathways. We investigated germline mutations in GNAI2, which encodes Gαi2, a key component in heterotrimeric G protein signal transduction usually thought to regulate adenylyl cyclase-mediated cyclic adenosine monophosphate (cAMP) production. Patients with activating Gαi2 mutations had clinical presentations that included impaired immunity. Mutant Gαi2 impaired cell migration and augmented responses to T cell receptor (TCR) stimulation. We found that mutant Gαi2 influenced TCR signaling by sequestering the guanosine triphosphatase (GTPase)-activating protein RASA2, thereby promoting RAS activation and increasing downstream extracellular signal-regulated kinase (ERK)/mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3-kinase (PI3K)-AKT S6 signaling to drive cellular growth and proliferation.
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Affiliation(s)
- Hyoungjun Ham
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- Clinical Genomics Program, DIR, NIAID, NIH, Bethesda, MD, USA
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Huie Jing
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- Clinical Genomics Program, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Ian T Lamborn
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- Clinical Genomics Program, DIR, NIAID, NIH, Bethesda, MD, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Megan M Kober
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- Clinical Genomics Program, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Alexey Koval
- Department of Cell Physiology and Metabolism, Faculty of Medicine, Translational Research Center in Oncohaematology, University of Geneva, Geneva, Switzerland
| | - Yamina A Berchiche
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, USA
| | - D Eric Anderson
- Advanced Mass Spectrometry Facility, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Kirk M Druey
- Lung and Vascular Inflammation Section, Laboratory of Allergic Diseases, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Judith N Mandl
- Lymphocyte Biology Section, Laboratory of Immune System Biology, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, Nantes Université, Nantes, France
- L'Institut du Thorax, CHU Nantes, INSERM UMR 1087/CNRS UMR 6291, Nantes Université, Nantes, France
| | - Carlos R Ferreira
- Skeletal Genomics Unit, Metabolic Medicine Branch, DIR, National Human Genome Research Institute (NHGRI), NIH, Bethesda, MD, USA
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, DIR, NIAID, NIH, Bethesda, MD 20892, USA
| | - Meliha Karsak
- Neuronal and Cellular Signal Transduction, Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter J Mustillo
- Nationwide Children's Hospital, Columbus, OH, USA
- The Ohio State University College of Medicine, Columbus, OH, USA
| | - Juliana Teo
- Department of Haematology, The Children's Hospital Westmead, Sydney, New South Wales, Australia
| | - Zarazuela Zolkipli-Cunningham
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nicolas Chatron
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Institut NeuroMyoGène, Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - François Lecoquierre
- Université de Rouen Normandie, INSERM U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, Rouen, France
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology (OCICB), NIAID, NIH, Bethesda, MD, USA
| | - Jana Pachlopnik Schmid
- Division of Immunology, University Children's Hospital Zurich, Zurich, Switzerland
- Pediatric Immunology, University of Zurich, Zurich, Switzerland
| | - Douglas B Kuhns
- Neutrophil Monitoring Lab, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Xuehua Xu
- Chemotaxis Signal Section, Laboratory of Immunogenetics, DIR, NIAID, NIH, Rockville, MD, USA
| | - Fabian Hauck
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität (LMU), Munich, Germany
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
- Department of Pediatrics, Al-Sabah Hospital, Kuwait City, Kuwait
| | - Matias Wagner
- Institute of Human Genetics, Technical University Munich, School of Medicine and Health, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Pediatrics, Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, University Hospital of Munich, Munich, Germany
| | - Paulien A Terhal
- Division of Laboratories, Pharmacy and Biomedical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Mari Muurinen
- Folkhälsan Research Center, Genetics Research Program, Helsinki, Finland
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Vincent Barlogis
- APHM, La Timone Children's Hospital, Department of Pediatric Hematology, Immunology, and Oncology, Marseille, France
- Aix-Marseille University, EA 3279 Research Unit, Marseille, France
| | - Phillip Cruz
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology (OCICB), NIAID, NIH, Bethesda, MD, USA
| | - Jeffrey Danielson
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- Clinical Genomics Program, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals, NHS Foundation Trust, Headington, Oxford, UK
| | - Petra Loid
- Folkhälsan Research Center, Genetics Research Program, Helsinki, Finland
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Sebastian Rading
- Neuronal and Cellular Signal Transduction, Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Boris Keren
- Genetic Departement, Assistance Publique - Hôpitaux de Paris.Sorbonne University, Paris, France
- SeqOIA Laboratory, FMG2025, Paris, France
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Kol A Zarember
- Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Katharina Vill
- LMU University Hospital, Department of Pediatrics, Division of Pediatric Neurology, iSPZ Hauner MUC - Munich University Center for Children with Medical and Developmental Complexity, Dr. von Hauner Children's Hospital, Munich, Germany
| | - Lorraine Potocki
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Kenneth N Olivier
- Pulmonary Branch, Division of Intramural Research, DIR, National Heart Lung and Blood Institute (NHLBI), NIH, Bethesda, MD, USA
| | - Gaetan Lesca
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Institut NeuroMyoGène, Physiopathologie et Génétique du Neurone et du Muscle, CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - Laurence Faivre
- Génétique des Anomalies du Développement (GAD), UMR 1231, INSERM, Université Bourgogne-Franche Comté, Dijon, France
- Centre de Génétique et Centre de Référence "Anomalies du Développement et Syndromes Malformatifs de l'Inter-région Est", FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Melanie Wong
- Department of Allergy and Immunology, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, INSERM U1163, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
| | - Janet Chou
- Division of Immunology, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Maud Tusseau
- Genetics Department, Lyon University Hospital, Lyon, France
- The International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France
| | - Niki M Moutsopoulos
- Oral Immunity and Infection Section, DIR, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD, USA
| | - Helen F Matthews
- Clinical Genomics Program, DIR, NIAID, NIH, Bethesda, MD, USA
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Cas Simons
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Ryan J Taft
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia
- Illumina, San Diego, CA, USA
| | - Ariane Soldatos
- National Institute of Neurological Disorders and Stroke (NINDS), NIH, Bethesda, MD, USA
| | - Etienne Masle-Farquhar
- Immunogenomics Laboratory, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, NCI, NIH, Bethesda, MD, USA
| | - Robert Brink
- St. Vincent's Clinical School, UNSW, Sydney, NSW, Australia
- B Cell Biology Laboratory, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Danielle L Fink
- Neutrophil Monitoring Lab, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Heidi H Kong
- Cutaneous Microbiome and Inflammation Section, Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD, USA
| | - Juraj Kabat
- Biological Imaging Section, Research Technologies Branch, DIR, NIAID, NIH, Bethesda, MD 20892, USA
| | - Woo Sung Kim
- Chemotaxis Signal Section, Laboratory of Immunogenetics, DIR, NIAID, NIH, Rockville, MD, USA
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kazuyuki Meguro
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- Clinical Genomics Program, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Amy P Hsu
- Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Jingwen Gu
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology (OCICB), NIAID, NIH, Bethesda, MD, USA
| | - Jennifer Stoddard
- Immunology Service, Department of Laboratory Medicine, Clinical Center, NIH, Bethesda, MD, USA
| | - Benito Banos-Pinero
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Maria Slack
- Division of Allergy and Immunology, Department of Pediatrics, University of Rochester Medical Center and Golisano Children's Hospital, Rochester, NY, USA
| | - Giampaolo Trivellin
- Section on Endocrinology and Genetics (SEGEN), DIR, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, USA
| | - Benoît Mazel
- Centre de Génétique et Centre de Référence "Anomalies du Développement et Syndromes Malformatifs de l'Inter-région Est", FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, CHU Dijon Bourgogne, Dijon, France
| | - Maarja Soomann
- Division of Immunology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Samuel Li
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology (OCICB), NIAID, NIH, Bethesda, MD, USA
| | - Val J Watts
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Constantine A Stratakis
- Section on Endocrinology and Genetics (SEGEN), DIR, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), NIH, Bethesda, MD, USA
| | - Maria F Rodriguez-Quevedo
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Ange-Line Bruel
- Génétique des Anomalies du Développement (GAD), UMR 1231, INSERM, Université Bourgogne-Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Marita Lipsanen-Nyman
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Paul Saultier
- APHM, La Timone Children's Hospital, Department of Pediatric Hematology, Immunology, and Oncology, Marseille, France
- Aix-Marseille University, INSERM, National Research Institute for Agriculture, Food and Environment (INRAe), Cardiovascular and Nutrition Research Center (C2VN), Marseille, France
| | - Rashmi Jain
- Clinical Immunology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Daphne Lehalle
- AP-HP Sorbonne Université, UF de Génétique Clinique, Centre de Référence Maladies Rares des Anomalies du Développement et Syndromes Malformatifs, Hôpital Trousseau, Paris, France
| | - Daniel Torres
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- Clinical Genomics Program, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Kathleen E Sullivan
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sébastien Barbarot
- Department of Dermatology, CHU Nantes, INRAE, UMR 1280, PhAN, Nantes Université, Nantes, France
| | - Axel Neu
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yannis Duffourd
- Génétique des Anomalies du Développement (GAD), UMR 1231, INSERM, Université Bourgogne-Franche Comté, Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Morgan Similuk
- Centralized Sequencing Program, DIR, NIAID, NIH, Bethesda, MD, USA
| | | | | | - Stéphane Bézieau
- Service de Génétique Médicale, CHU Nantes, Nantes Université, Nantes, France
- L'Institut du Thorax, CHU Nantes, INSERM UMR 1087/CNRS UMR 6291, Nantes Université, Nantes, France
| | - Tian Jin
- Chemotaxis Signal Section, Laboratory of Immunogenetics, DIR, NIAID, NIH, Rockville, MD, USA
| | - Raif S Geha
- Division of Immunology, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, INSERM U1163, Paris, France
- Imagine Institute, University of Paris Cité, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
| | - Outi M Makitie
- Folkhälsan Research Center, Genetics Research Program, Helsinki, Finland
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Patrick Edery
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
- Centre de Recherche en Neurosciences de Lyon, Inserm U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France
| | - John Christodoulou
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
- Specialty of Child and Adolescent Health, University of Sydney, Sydney, Australia
| | - Ronald N Germain
- Lymphocyte Biology Section, Laboratory of Immune System Biology, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Christopher C Goodnow
- Immunogenomics Laboratory, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Cellular Genomics Futures Institute, Sydney, NSW, Australia
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, USA
- Karolinska Institutet, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Division of Neurogeriatrics, Stockholm, Sweden
| | - Daniel D Billadeau
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, Nantes Université, Nantes, France
- L'Institut du Thorax, CHU Nantes, INSERM UMR 1087/CNRS UMR 6291, Nantes Université, Nantes, France
| | - Vladimir L Katanaev
- Department of Cell Physiology and Metabolism, Faculty of Medicine, Translational Research Center in Oncohaematology, University of Geneva, Geneva, Switzerland
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- Clinical Genomics Program, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Michael J Lenardo
- Clinical Genomics Program, DIR, NIAID, NIH, Bethesda, MD, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, DIR, NIAID, NIH, Bethesda, MD, USA
| | - Helen C Su
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research (DIR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- Clinical Genomics Program, DIR, NIAID, NIH, Bethesda, MD, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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5
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Arici MK, Tuncbag N. Unveiling hidden connections in omics data via pyPARAGON: an integrative hybrid approach for disease network construction. Brief Bioinform 2024; 25:bbae399. [PMID: 39163205 PMCID: PMC11334722 DOI: 10.1093/bib/bbae399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 06/26/2024] [Accepted: 08/07/2024] [Indexed: 08/22/2024] Open
Abstract
Network inference or reconstruction algorithms play an integral role in successfully analyzing and identifying causal relationships between omics hits for detecting dysregulated and altered signaling components in various contexts, encompassing disease states and drug perturbations. However, accurate representation of signaling networks and identification of context-specific interactions within sparse omics datasets in complex interactomes pose significant challenges in integrative approaches. To address these challenges, we present pyPARAGON (PAgeRAnk-flux on Graphlet-guided network for multi-Omic data integratioN), a novel tool that combines network propagation with graphlets. pyPARAGON enhances accuracy and minimizes the inclusion of nonspecific interactions in signaling networks by utilizing network rather than relying on pairwise connections among proteins. Through comprehensive evaluations on benchmark signaling pathways, we demonstrate that pyPARAGON outperforms state-of-the-art approaches in node propagation and edge inference. Furthermore, pyPARAGON exhibits promising performance in discovering cancer driver networks. Notably, we demonstrate its utility in network-based stratification of patient tumors by integrating phosphoproteomic data from 105 breast cancer tumors with the interactome and demonstrating tumor-specific signaling pathways. Overall, pyPARAGON is a novel tool for analyzing and integrating multi-omic data in the context of signaling networks. pyPARAGON is available at https://github.com/netlab-ku/pyPARAGON.
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Affiliation(s)
- Muslum Kaan Arici
- Graduate School of Informatics, Middle East Technical University, Ankara 06800, Turkey
| | - Nurcan Tuncbag
- Chemical and Biological Engineering, College of Engineering, Koc University, Istanbul 34450, Turkey
- School of Medicine, Koc University, Istanbul 34450, Turkey
- Koc University Research Center for Translational Medicine (KUTTAM), Koc University, Istanbul 34450, Turkey
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6
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Bukaeva A, Myasnikov R, Kulikova O, Meshkov A, Kiseleva A, Petukhova A, Zotova E, Sparber P, Ershova A, Sotnikova E, Kudryavtseva M, Zharikova A, Koretskiy S, Mershina E, Ramensky V, Zaicenoka M, Vyatkin Y, Muraveva A, Abisheva A, Nikityuk T, Sinitsyn V, Divashuk M, Dadali E, Pokrovskaya M, Drapkina O. A Rare Coincidence of Three Inherited Diseases in a Family with Cardiomyopathy and Multiple Extracardiac Abnormalities. Int J Mol Sci 2024; 25:7556. [PMID: 39062799 PMCID: PMC11277405 DOI: 10.3390/ijms25147556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
A genetic diagnosis of primary cardiomyopathies can be a long-unmet need in patients with complex phenotypes. We investigated a three-generation family with cardiomyopathy and various extracardiac abnormalities that had long sought a precise diagnosis. The 41-year-old proband had hypertrophic cardiomyopathy (HCM), left ventricular noncompaction, myocardial fibrosis, arrhythmias, and a short stature. His sister showed HCM, myocardial hypertrabeculation and fibrosis, sensorineural deafness, and congenital genitourinary malformations. Their father had left ventricular hypertrophy (LVH). The proband's eldest daughter demonstrated developmental delay and seizures. We performed a clinical examination and whole-exome sequencing for all available family members. All patients with HCM/LVH shared a c.4411-2A>C variant in ALPK3, a recently known HCM-causative gene. Functional studies confirmed that this variant alters ALPK3 canonical splicing. Due to extracardiac symptoms in the female patients, we continued the search and found two additional single-gene disorders. The proband's sister had a p.Trp329Gly missense in GATA3, linked to hypoparathyroidism, sensorineural deafness, and renal dysplasia; his daughter had a p.Ser251del in WDR45, associated with beta-propeller protein-associated neurodegeneration. This unique case of three monogenic disorders in one family shows how a comprehensive approach with thorough phenotyping and extensive genetic testing of all symptomatic individuals provides precise diagnoses and appropriate follow-up, embodying the concept of personalized medicine. We also present the first example of a splicing functional study for ALPK3 and describe the genotype-phenotype correlations in cardiomyopathy.
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Affiliation(s)
- Anna Bukaeva
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
| | - Roman Myasnikov
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
| | - Olga Kulikova
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
| | - Alexey Meshkov
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
- National Medical Research Center of Cardiology, 121552 Moscow, Russia
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.S.); (E.D.)
- Department of General and Medical Genetics, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Anna Kiseleva
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
| | - Anna Petukhova
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
| | - Evgenia Zotova
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
| | - Peter Sparber
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.S.); (E.D.)
| | - Alexandra Ershova
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
| | - Evgeniia Sotnikova
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
| | - Maria Kudryavtseva
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
| | - Anastasia Zharikova
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sergey Koretskiy
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
| | - Elena Mershina
- Medical Research and Educational Center, Lomonosov Moscow State University, 119991 Moscow, Russia; (E.M.); (V.S.)
| | - Vasily Ramensky
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
- MSU Institute for Artificial Intelligence, Lomonosov Moscow State University, 119991 Moscow, Russia
| | | | - Yuri Vyatkin
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
- MSU Institute for Artificial Intelligence, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alisa Muraveva
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
| | - Alexandra Abisheva
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
| | - Tatiana Nikityuk
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
| | - Valentin Sinitsyn
- Medical Research and Educational Center, Lomonosov Moscow State University, 119991 Moscow, Russia; (E.M.); (V.S.)
| | - Mikhail Divashuk
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Elena Dadali
- Research Centre for Medical Genetics, 115522 Moscow, Russia; (P.S.); (E.D.)
| | - Maria Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
| | - Oxana Drapkina
- National Medical Research Center for Therapy and Preventive Medicine, 101990 Moscow, Russia; (R.M.); (O.K.); (A.M.); (A.K.); (A.P.); (E.Z.); (A.E.); (E.S.); (M.K.); (A.Z.); (S.K.); (V.R.); (Y.V.); (A.M.); (A.A.); (T.N.); (M.D.); (M.P.); (O.D.)
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7
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Kansal R. The CRISPR-Cas System and Clinical Applications of CRISPR-Based Gene Editing in Hematology with a Focus on Inherited Germline Predisposition to Hematologic Malignancies. Genes (Basel) 2024; 15:863. [PMID: 39062641 PMCID: PMC11276294 DOI: 10.3390/genes15070863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing has begun to transform the treatment landscape of genetic diseases. The history of the discovery of CRISPR/CRISPR-associated (Cas) proteins/single-guide RNA (sgRNA)-based gene editing since the first report of repetitive sequences of unknown significance in 1987 is fascinating, highly instructive, and inspiring for future advances in medicine. The recent approval of CRISPR-Cas9-based gene therapy to treat patients with severe sickle cell anemia and transfusion-dependent β-thalassemia has renewed hope for treating other hematologic diseases, including patients with a germline predisposition to hematologic malignancies, who would benefit greatly from the development of CRISPR-inspired gene therapies. The purpose of this paper is three-fold: first, a chronological description of the history of CRISPR-Cas9-sgRNA-based gene editing; second, a brief description of the current state of clinical research in hematologic diseases, including selected applications in treating hematologic diseases with CRISPR-based gene therapy, preceded by a brief description of the current tools being used in clinical genome editing; and third, a presentation of the current progress in gene therapies in inherited hematologic diseases and bone marrow failure syndromes, to hopefully stimulate efforts towards developing these therapies for patients with inherited bone marrow failure syndromes and other inherited conditions with a germline predisposition to hematologic malignancies.
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Affiliation(s)
- Rina Kansal
- Molecular Oncology and Genetics, Diagnostic Laboratories, Versiti Blood Center of Wisconsin, Milwaukee, WI 53233, USA;
- Department of Pathology and Anatomical Sciences, The University at Buffalo, Buffalo, NY 14260, USA
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8
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Fuentes-Mateos R, García-Navas R, Fernández-Infante C, Hernández-Cano L, Calzada-Nieto N, Juan AOS, Guerrero C, Santos E, Fernández-Medarde A. Combined HRAS and NRAS ablation induces a RASopathy phenotype in mice. Cell Commun Signal 2024; 22:332. [PMID: 38886790 PMCID: PMC11184836 DOI: 10.1186/s12964-024-01717-4] [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: 02/05/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND HRASKO/NRASKO double knockout mice exhibit exceedingly high rates of perinatal lethality due to respiratory failure caused by a significant lung maturation delay. The few animals that reach adulthood have a normal lifespan, but present areas of atelectasis mixed with patches of emphysema and normal tissue in the lung. METHODS Eight double knockout and eight control mice were analyzed using micro-X-ray computerized tomography and a Small Animal Physiological Monitoring system. Tissues and samples from these mice were analyzed using standard histological and Molecular Biology methods and the significance of the results analyzed using a Student´s T-test. RESULTS The very few double knockout mice surviving up to adulthood display clear craniofacial abnormalities reminiscent of those seen in RASopathy mouse models, as well as thrombocytopenia, bleeding anomalies, and reduced platelet activation induced by thrombin. These surviving mice also present heart and spleen hyperplasia, and elevated numbers of myeloid-derived suppressor cells in the spleen. Mechanistically, we observed that these phenotypic alterations are accompanied by increased KRAS-GTP levels in heart, platelets and primary mouse embryonic fibroblasts from these animals. CONCLUSIONS Our data uncovers a new, previously unidentified mechanism capable of triggering a RASopathy phenotype in mice as a result of the combined removal of HRAS and NRAS.
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Affiliation(s)
- Rocío Fuentes-Mateos
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca) and CIBERONC, Campus Unamuno, University of Salamanca, 37007, Salamanca, Spain
- Present address: Department of Molecular Pharmacology, Groningen Research Institute for Asthma and COPD, University of Groningen, Groningen, Netherlands
| | - Rósula García-Navas
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca) and CIBERONC, Campus Unamuno, University of Salamanca, 37007, Salamanca, Spain
| | - Cristina Fernández-Infante
- Instituto de Biología Molecular y Celular del Cáncer (IMBCC), USAL-CSIC. Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
| | - Luis Hernández-Cano
- Instituto de Biología Molecular y Celular del Cáncer (IMBCC), USAL-CSIC. Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
- Present address: Department of Nuclear Medicine and Molecular Imaging, University Medical Center Groningen, Groningen, Netherlands
| | - Nuria Calzada-Nieto
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca) and CIBERONC, Campus Unamuno, University of Salamanca, 37007, Salamanca, Spain
| | - Andrea Olarte-San Juan
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca) and CIBERONC, Campus Unamuno, University of Salamanca, 37007, Salamanca, Spain
| | - Carmen Guerrero
- Instituto de Biología Molecular y Celular del Cáncer (IMBCC), USAL-CSIC. Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
- Departamento de Medicina, Universidad de Salamanca, Salamanca, Spain
| | - Eugenio Santos
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca) and CIBERONC, Campus Unamuno, University of Salamanca, 37007, Salamanca, Spain.
| | - Alberto Fernández-Medarde
- Centro de Investigación del Cáncer-Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca) and CIBERONC, Campus Unamuno, University of Salamanca, 37007, Salamanca, Spain.
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9
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Lazea C, Vulturar R, Chiș A, Encica S, Horvat M, Belizna C, Damian LO. Macrocephaly and Finger Changes: A Narrative Review. Int J Mol Sci 2024; 25:5567. [PMID: 38791606 PMCID: PMC11122644 DOI: 10.3390/ijms25105567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
Macrocephaly, characterized by an abnormally large head circumference, often co-occurs with distinctive finger changes, presenting a diagnostic challenge for clinicians. This review aims to provide a current synthetic overview of the main acquired and genetic etiologies associated with macrocephaly and finger changes. The genetic cause encompasses several categories of diseases, including bone marrow expansion disorders, skeletal dysplasias, ciliopathies, inherited metabolic diseases, RASopathies, and overgrowth syndromes. Furthermore, autoimmune and autoinflammatory diseases are also explored for their potential involvement in macrocephaly and finger changes. The intricate genetic mechanisms involved in the formation of cranial bones and extremities are multifaceted. An excess in growth may stem from disruptions in the intricate interplays among the genetic, epigenetic, and hormonal factors that regulate human growth. Understanding the underlying cellular and molecular mechanisms is important for elucidating the developmental pathways and biological processes that contribute to the observed clinical phenotypes. The review provides a practical approach to delineate causes of macrocephaly and finger changes, facilitate differential diagnosis and guide for the appropriate etiological framework. Early recognition contributes to timely intervention and improved outcomes for affected individuals.
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Affiliation(s)
- Cecilia Lazea
- 1st Department of Pediatrics, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, 400370 Cluj-Napoca, Romania;
- 1st Pediatrics Clinic, Emergency Pediatric Clinical Hospital, 400370 Cluj-Napoca, Romania
| | - Romana Vulturar
- Department of Molecular Sciences, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, 400349 Cluj-Napoca, Romania;
- Cognitive Neuroscience Laboratory, University Babes-Bolyai, 400015 Cluj-Napoca, Romania
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St., 400497 Cluj-Napoca, Romania;
| | - Adina Chiș
- Department of Molecular Sciences, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, 400349 Cluj-Napoca, Romania;
- Cognitive Neuroscience Laboratory, University Babes-Bolyai, 400015 Cluj-Napoca, Romania
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St., 400497 Cluj-Napoca, Romania;
| | - Svetlana Encica
- Department of Pathology, “Niculae Stancioiu” Heart Institute Cluj-Napoca, 19-21 Calea Moților St., 400001 Cluj-Napoca, Romania;
| | - Melinda Horvat
- Department of Infectious Diseases and Epidemiology, The Clinical Hospital of Infectious Diseases, “Iuliu Hatieganu” University of Medicine and Pharmacy Cluj-Napoca, 400348 Cluj-Napoca, Romania;
| | - Cristina Belizna
- UMR CNRS 6015, INSERM U1083, University of Angers, 49100 Angers, France;
- Internal Medicine Department Clinique de l’Anjou, Vascular and Coagulation Department, University Hospital Angers, 49100 Angers, France
| | - Laura-Otilia Damian
- Association for Innovation in Rare Inflammatory, Metabolic, Genetic Diseases INNOROG, 30E, Făgetului St., 400497 Cluj-Napoca, Romania;
- Department of Rheumatology, Center for Rare Musculoskeletal Autoimmune and Autoinflammatory Diseases, Emergency Clinical County Hospital Cluj, 400006 Cluj-Napoca, Romania
- CMI Reumatologie Dr. Damian, 400002 Cluj-Napoca, Romania
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10
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Choi JK, Xiao W, Chen X, Loghavi S, Elenitoba-Johnson KS, Naresh KN, Medeiros LJ, Czader M. Fifth Edition of the World Health Organization Classification of Tumors of the Hematopoietic and Lymphoid Tissues: Acute Lymphoblastic Leukemias, Mixed-Phenotype Acute Leukemias, Myeloid/Lymphoid Neoplasms With Eosinophilia, Dendritic/Histiocytic Neoplasms, and Genetic Tumor Syndromes. Mod Pathol 2024; 37:100466. [PMID: 38460674 DOI: 10.1016/j.modpat.2024.100466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/11/2024] [Accepted: 03/01/2024] [Indexed: 03/11/2024]
Abstract
This manuscript represents a review of lymphoblastic leukemia/lymphoma (acute lymphoblastic leukemia/lymphoblastic lymphoma), acute leukemias of ambiguous lineage, mixed-phenotype acute leukemias, myeloid/lymphoid neoplasms with eosinophilia and defining gene rearrangements, histiocytic and dendritic neoplasms, and genetic tumor syndromes of the 5th edition of the World Health Organization Classification of Tumors of the Hematopoietic and Lymphoid Tissues. The diagnostic, clinicopathologic, cytogenetic, and molecular genetic features are discussed. The differences in comparison to the 4th revised edition of the World Health Organization classification of hematolymphoid neoplasms are highlighted.
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Affiliation(s)
- John K Choi
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xueyan Chen
- Section of Pathology, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Sanam Loghavi
- Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas
| | - Kojo S Elenitoba-Johnson
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kikkeri N Naresh
- Section of Pathology, Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - L Jeffrey Medeiros
- Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas
| | - Magdalena Czader
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana.
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11
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Padhiyar J, Mahajan R, Panda M. RASopathies: Evolving Concepts in Pathogenetics, Clinical Features, and Management. Indian Dermatol Online J 2024; 15:392-404. [PMID: 38845651 PMCID: PMC11152490 DOI: 10.4103/idoj.idoj_594_23] [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: 08/03/2023] [Revised: 09/27/2023] [Accepted: 10/01/2023] [Indexed: 06/09/2024] Open
Abstract
RASopathies refers to the group of disorders which are caused by a mutation in various genes of the RAS/MAPK (RAT sarcoma virus/Mitogen activated protein kinase) pathway. It includes many genes with varied functions, which are responsible for cell cycle regulation. As the mutation in one gene affects the entire pathway, there are many overlapping features among the various syndromes which are included under an umbrella term "RASopathies." However, neuroectodermal involvement is a unifying feature among these syndromes, which are caused by germline mutations affecting genes along this pathway. Recently, many other RASopathies have been described to involve blood vessels, lymphatics, and immune system. Also, many cutaneous mosaic disorders have been found to have mutations in the concerned pathway. The purpose of this article is to briefly review the pathogenesis of RASopathies with cutaneous manifestations, and summarise the features that can be helpful as diagnostic clues to dermatologists. As we understand more about the pathogenesis of the pathway at the cellular level, the research on genotype-phenotype correlation and therapeutic options broadens. Targeted therapy is in the clinical and preclinical trial phase, which may brighten the future of many patients.
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Affiliation(s)
- Jigna Padhiyar
- Department of DVL, Gujarat Cancer Society Medical College, Hospital and Research Centre, Ahmedabad, Gujarat, India
| | - Rahul Mahajan
- Department of Dermatology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Maitreyee Panda
- Department of Dermatology, IMS and SUM Hospital, Bhubaneshwar, Odisha, India
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12
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Lin HT, Takagi M, Kubara K, Yamazaki K, Michikawa F, Okumura T, Naruto T, Morio T, Miyazaki K, Taniguchi H, Otsu M. Monoallelic KRAS (G13C) mutation triggers dysregulated expansion in induced pluripotent stem cell-derived hematopoietic progenitor cells. Stem Cell Res Ther 2024; 15:106. [PMID: 38627844 PMCID: PMC11021011 DOI: 10.1186/s13287-024-03723-2] [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: 01/25/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Although oncogenic RAS mutants are thought to exert mutagenic effects upon blood cells, it remains uncertain how a single oncogenic RAS impacts non-transformed multipotent hematopoietic stem or progenitor cells (HPCs). Such potential pre-malignant status may characterize HPCs in patients with RAS-associated autoimmune lymphoproliferative syndrome-like disease (RALD). This study sought to elucidate the biological and molecular alterations in human HPCs carrying monoallelic mutant KRAS (G13C) with no other oncogene mutations. METHODS We utilized induced pluripotent stem cells (iPSCs) derived from two unrelated RALD patients. Isogenic HPC pairs harboring either wild-type KRAS or monoallelic KRAS (G13C) alone obtained following differentiation enabled reliable comparative analyses. The compound screening was conducted with an established platform using KRAS (G13C) iPSCs and differentiated HPCs. RESULTS Cell culture assays revealed that monoallelic KRAS (G13C) impacted both myeloid differentiation and expansion characteristics of iPSC-derived HPCs. Comprehensive RNA-sequencing analysis depicted close clustering of HPC samples within the isogenic group, warranting that comparative studies should be performed within the same genetic background. When compared with no stimulation, iPSC-derived KRAS (G13C)-HPCs showed marked similarity with the wild-type isogenic control in transcriptomic profiles. After stimulation with cytokines, however, KRAS (G13C)-HPCs exhibited obvious aberrant cell-cycle and apoptosis responses, compatible with "dysregulated expansion," demonstrated by molecular and biological assessment. Increased BCL-xL expression was identified amongst other molecular changes unique to mutant HPCs. With screening platforms established for therapeutic intervention, we observed selective activity against KRAS (G13C)-HPC expansion in several candidate compounds, most notably in a MEK- and a BCL-2/BCL-xL-inhibitor. These two compounds demonstrated selective inhibitory effects on KRAS (G13C)-HPCs even with primary patient samples when combined. CONCLUSIONS Our findings indicate that a monoallelic oncogenic KRAS can confer dysregulated expansion characteristics to non-transformed HPCs, which may constitute a pathological condition in RALD hematopoiesis. The use of iPSC-based screening platforms will lead to discovering treatments that enable selective inhibition of RAS-mutated HPC clones.
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Affiliation(s)
- Huan-Ting Lin
- Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan.
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Kenji Kubara
- Tsukuba Research Laboratories, Eisai Co., Ltd., Tsukuba, Ibaraki, 300-2635, Japan
| | - Kazuto Yamazaki
- Tsukuba Research Laboratories, Eisai Co., Ltd., Tsukuba, Ibaraki, 300-2635, Japan
| | - Fumiko Michikawa
- Tsukuba Research Laboratories, Eisai Co., Ltd., Tsukuba, Ibaraki, 300-2635, Japan
| | - Takashi Okumura
- Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - Takuya Naruto
- Department of Pediatrics and Developmental Biology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, 113-8519, Japan
| | - Koji Miyazaki
- Department of Transfusion and Cell Transplantation, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan
| | - Hideki Taniguchi
- Division of Regenerative Medicine, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
- Department of Regenerative Medicine, Graduate School of Medicine, Yokohama City University, Yokohama, Kanagawa, 236-0004, Japan
| | - Makoto Otsu
- Department of Transfusion and Cell Transplantation, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0374, Japan.
- Division of Hematology, Department of Medical Laboratory Sciences, Kitasato University School of Medicine, Sagamihara, Kanagawa, 252-0373, Japan.
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13
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Juchnewitsch AG, Pomm K, Dutta A, Tamp E, Valkna A, Lillepea K, Mahyari E, Tjagur S, Belova G, Kübarsepp V, Castillo-Madeen H, Riera-Escamilla A, Põlluaas L, Nagirnaja L, Poolamets O, Vihljajev V, Sütt M, Versbraegen N, Papadimitriou S, McLachlan RI, Jarvi KA, Schlegel PN, Tennisberg S, Korrovits P, Vigh-Conrad K, O’Bryan MK, Aston KI, Lenaerts T, Conrad DF, Kasak L, Punab M, Laan M. Undiagnosed RASopathies in infertile men. Front Endocrinol (Lausanne) 2024; 15:1312357. [PMID: 38654924 PMCID: PMC11035881 DOI: 10.3389/fendo.2024.1312357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/11/2024] [Indexed: 04/26/2024] Open
Abstract
RASopathies are syndromes caused by congenital defects in the Ras/mitogen-activated protein kinase (MAPK) pathway genes, with a population prevalence of 1 in 1,000. Patients are typically identified in childhood based on diverse characteristic features, including cryptorchidism (CR) in >50% of affected men. As CR predisposes to spermatogenic failure (SPGF; total sperm count per ejaculate 0-39 million), we hypothesized that men seeking infertility management include cases with undiagnosed RASopathies. Likely pathogenic or pathogenic (LP/P) variants in 22 RASopathy-linked genes were screened in 521 idiopathic SPGF patients (including 155 CR cases) and 323 normozoospermic controls using exome sequencing. All 844 men were recruited to the ESTonian ANDrology (ESTAND) cohort and underwent identical andrological phenotyping. RASopathy-specific variant interpretation guidelines were used for pathogenicity assessment. LP/P variants were identified in PTPN11 (two), SOS1 (three), SOS2 (one), LZTR1 (one), SPRED1 (one), NF1 (one), and MAP2K1 (one). The findings affected six of 155 cases with CR and SPGF, three of 366 men with SPGF only, and one (of 323) normozoospermic subfertile man. The subgroup "CR and SPGF" had over 13-fold enrichment of findings compared to controls (3.9% vs. 0.3%; Fisher's exact test, p = 5.5 × 10-3). All ESTAND subjects with LP/P variants in the Ras/MAPK pathway genes presented congenital genitourinary anomalies, skeletal and joint conditions, and other RASopathy-linked health concerns. Rare forms of malignancies (schwannomatosis and pancreatic and testicular cancer) were reported on four occasions. The Genetics of Male Infertility Initiative (GEMINI) cohort (1,416 SPGF cases and 317 fertile men) was used to validate the outcome. LP/P variants in PTPN11 (three), LZTR1 (three), and MRAS (one) were identified in six SPGF cases (including 4/31 GEMINI cases with CR) and one normozoospermic man. Undiagnosed RASopathies were detected in total for 17 ESTAND and GEMINI subjects, 15 SPGF patients (10 with CR), and two fertile men. Affected RASopathy genes showed high expression in spermatogenic and testicular somatic cells. In conclusion, congenital defects in the Ras/MAPK pathway genes represent a new congenital etiology of syndromic male infertility. Undiagnosed RASopathies were especially enriched among patients with a history of cryptorchidism. Given the relationship between RASopathies and other conditions, infertile men found to have this molecular diagnosis should be evaluated for known RASopathy-linked health concerns, including specific rare malignancies.
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Affiliation(s)
- Anna-Grete Juchnewitsch
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kristjan Pomm
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Avirup Dutta
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Erik Tamp
- Centre of Pathology, East Tallinn Central Hospital, Tallinn, Estonia
| | - Anu Valkna
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kristiina Lillepea
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Eisa Mahyari
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | | | - Galina Belova
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Viljo Kübarsepp
- Department of Surgery, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Pediatric Surgery, Clinic of Surgery, Tartu University Hospital, Tartu, Estonia
| | - Helen Castillo-Madeen
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Antoni Riera-Escamilla
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Lisanna Põlluaas
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Olev Poolamets
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
| | | | - Mailis Sütt
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Nassim Versbraegen
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Sofia Papadimitriou
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Science, Ghent University, Ghent, Belgium
| | - Robert I. McLachlan
- Hudson Institute of Medical Research and the Department of Obstetrics and Gynecology, Monash University, Clayton, VIC, Australia
| | - Keith A. Jarvi
- Division of Urology, Department of Surgery, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Peter N. Schlegel
- Department of Urology, Weill Cornell Medical College, New York, NY, United States
| | | | - Paul Korrovits
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Katinka Vigh-Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Moira K. O’Bryan
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Kenneth I. Aston
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - Donald F. Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
- Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Beaverton, OR, United States
| | - Laura Kasak
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Margus Punab
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Surgery, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Maris Laan
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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14
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Benetti A, Bertozzi I, Ceolotto G, Cortella I, Regazzo D, Biagetti G, Cosi E, Randi ML. Coexistence of Multiple Gene Variants in Some Patients with Erythrocytoses. Mediterr J Hematol Infect Dis 2024; 16:e2024021. [PMID: 38468832 PMCID: PMC10927185 DOI: 10.4084/mjhid.2024.021] [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] [Received: 11/03/2023] [Accepted: 02/10/2024] [Indexed: 03/13/2024] Open
Abstract
Background Erythrocytosis is a relatively common condition; however, a large proportion of these patients (70%) remain without a clear etiologic explanation. Methods We set up a targeted NGS panel for patients with erythrocytosis, and 118 sporadic patients with idiopathic erythrocytosis were studied. Results In 40 (34%) patients, no variant was found, while in 78 (66%), we identified at least one germinal variant; 55 patients (70.5%) had 1 altered gene, 18 (23%) had 2 alterations, and 5 (6.4%) had 3. An altered HFE gene was observed in 51 cases (57.1%), EGLN1 in 18 (22.6%) and EPAS1, EPOR, JAK2, and TFR2 variants in 7.7%, 10.3%, 11.5%, and 14.1% patients, respectively. In 23 patients (19.45%), more than 1 putative variant was found in multiple genes. Conclusions Genetic variants in patients with erythrocytosis were detected in about 2/3 of our cohort. An NGS panel including more candidate genes should reduce the number of cases diagnosed as "idiopathic" erythrocytosis in which a cause cannot yet be identified. It is known that HFE variants are common in idiopathic erythrocytosis. TFR2 alterations support the existence of a relationship between genes involved in iron metabolism and impaired erythropoiesis. Some novel multiple variants were identified. Erythrocytosis appears to be often multigenic.
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Affiliation(s)
- Andrea Benetti
- First Medical Clinic, Department of Medicine – DIMED, University of Padova, Padova, Italy
| | - Irene Bertozzi
- First Medical Clinic, Department of Medicine – DIMED, University of Padova, Padova, Italy
| | - Giulio Ceolotto
- Emergency Medicine, Department of Medicine – DIMED, University of Padova, Padova, Italy
| | - Irene Cortella
- First Medical Clinic, Department of Medicine – DIMED, University of Padova, Padova, Italy
| | - Daniela Regazzo
- First Medical Clinic, Department of Medicine – DIMED, University of Padova, Padova, Italy
| | - Giacomo Biagetti
- First Medical Clinic, Department of Medicine – DIMED, University of Padova, Padova, Italy
| | - Elisabetta Cosi
- First Medical Clinic, Department of Medicine – DIMED, University of Padova, Padova, Italy
| | - Maria Luigia Randi
- First Medical Clinic, Department of Medicine – DIMED, University of Padova, Padova, Italy
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15
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Rivalta B, Attardi E, Cifaldi C, Rosti V, Pacillo L, Hajrullaj H, Di Cesare S, Amodio D, Algeri M, Luciani M, Barzaghi F, Finocchi A, Di Matteo G, Aiuti A, Locatelli F, Voso MT, Palumbo G, Cancrini C. Natural history of Ras-associated autoimmune leukoproliferative disorder: A 20-year follow-up of a NRAS-mutated patient excluding a malignant progression. Br J Haematol 2024; 204:e6-e10. [PMID: 37921255 DOI: 10.1111/bjh.19150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 11/04/2023]
Affiliation(s)
- B Rivalta
- Research Unit of Primary Immunodeficiencies, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, Scientific Institute for Research and Healthcare (IRCCS), Rome, Italy
- PhD Program in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - E Attardi
- PhD Program in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - C Cifaldi
- Research Unit of Primary Immunodeficiencies, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, Scientific Institute for Research and Healthcare (IRCCS), Rome, Italy
| | - V Rosti
- Center for the Study of Myelofibrosis, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | - L Pacillo
- Research Unit of Primary Immunodeficiencies, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, Scientific Institute for Research and Healthcare (IRCCS), Rome, Italy
- PhD Program in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - H Hajrullaj
- PhD Program in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - S Di Cesare
- Research Unit of Primary Immunodeficiencies, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, Scientific Institute for Research and Healthcare (IRCCS), Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - D Amodio
- Research Unit of Primary Immunodeficiencies, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, Scientific Institute for Research and Healthcare (IRCCS), Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - M Algeri
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, Scientific Institute for Research and Healthcare (IRCCS), Rome, Italy
| | - M Luciani
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, Scientific Institute for Research and Healthcare (IRCCS), Rome, Italy
| | - F Barzaghi
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - A Finocchi
- Research Unit of Primary Immunodeficiencies, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, Scientific Institute for Research and Healthcare (IRCCS), Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - G Di Matteo
- Research Unit of Primary Immunodeficiencies, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, Scientific Institute for Research and Healthcare (IRCCS), Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - A Aiuti
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - F Locatelli
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, Scientific Institute for Research and Healthcare (IRCCS), Rome, Italy
- Department of Life Sciences and Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - M T Voso
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - G Palumbo
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, Bambino Gesù Children's Hospital, Scientific Institute for Research and Healthcare (IRCCS), Rome, Italy
| | - C Cancrini
- Research Unit of Primary Immunodeficiencies, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, Scientific Institute for Research and Healthcare (IRCCS), Rome, Italy
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
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16
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Onore ME, Caiazza M, Farina A, Scarano G, Budillon A, Borrelli RN, Limongelli G, Nigro V, Piluso G. A Novel Homozygous Loss-of-Function Variant in SPRED2 Causes Autosomal Recessive Noonan-like Syndrome. Genes (Basel) 2023; 15:32. [PMID: 38254922 PMCID: PMC10815364 DOI: 10.3390/genes15010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Noonan syndrome is an autosomal dominant developmental disorder characterized by peculiar facial dysmorphisms, short stature, congenital heart defects, and hypertrophic cardiomyopathy. In 2001, PTPN11 was identified as the first Noonan syndrome gene and is responsible for the majority of Noonan syndrome cases. Over the years, several other genes involved in Noonan syndrome (KRAS, SOS1, RAF1, MAP2K1, BRAF, NRAS, RIT1, and LZTR1) have been identified, acting at different levels of the RAS-mitogen-activated protein kinase pathway. Recently, SPRED2 was recognized as a novel Noonan syndrome gene with autosomal recessive inheritance, and only four families have been described to date. Here, we report the first Italian case, a one-year-old child with left ventricular hypertrophy, moderate pulmonary valve stenosis, and atrial septal defect, with a clinical suspicion of RASopathy supported by the presence of typical Noonan-like facial features and short stature. Exome sequencing identified a novel homozygous loss-of-function variant in the exon 3 of SPRED2 (NM_181784.3:c.325del; p.Arg109Glufs*7), likely causing nonsense-mediated decay. Our results and the presented clinical data may help us to further understand and dissect the genetic heterogeneity of Noonan syndrome.
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Affiliation(s)
- Maria Elena Onore
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.E.O.); (A.F.); (A.B.); (R.N.B.); (V.N.)
| | - Martina Caiazza
- Inherited and Rare Cardiovascular Diseases Unit, Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, Monaldi Hospital, 80131 Naples, Italy; (M.C.); (G.S.); (G.L.)
| | - Antonella Farina
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.E.O.); (A.F.); (A.B.); (R.N.B.); (V.N.)
| | - Gioacchino Scarano
- Inherited and Rare Cardiovascular Diseases Unit, Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, Monaldi Hospital, 80131 Naples, Italy; (M.C.); (G.S.); (G.L.)
- Medical Genetics Unit, AORN “San Pio”, Hospital “G. Rummo”, 82100 Benevento, Italy
| | - Alberto Budillon
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.E.O.); (A.F.); (A.B.); (R.N.B.); (V.N.)
| | - Rossella Nicoletta Borrelli
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.E.O.); (A.F.); (A.B.); (R.N.B.); (V.N.)
| | - Giuseppe Limongelli
- Inherited and Rare Cardiovascular Diseases Unit, Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, Monaldi Hospital, 80131 Naples, Italy; (M.C.); (G.S.); (G.L.)
- Institute of Cardiovascular Science, University College London and St. Bartholomew’s Hospital, London E1 4NS, UK
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.E.O.); (A.F.); (A.B.); (R.N.B.); (V.N.)
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Giulio Piluso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (M.E.O.); (A.F.); (A.B.); (R.N.B.); (V.N.)
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17
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Wang D, Wen X, Xu LL, Chen QX, Yan TX, Xiao HT, Xu XW. Nf1 in heart development: a potential causative gene for congenital heart disease: a narrative review. Physiol Genomics 2023; 55:415-426. [PMID: 37519249 DOI: 10.1152/physiolgenomics.00024.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/26/2023] [Accepted: 07/08/2023] [Indexed: 08/01/2023] Open
Abstract
Congenital heart disease is the most frequent congenital disorder, affecting a significant number of live births. Gaining insights into its genetic etiology could lead to a deeper understanding of this condition. Although the Nf1 gene has been identified as a potential causative gene, its role in congenital heart disease has not been thoroughly clarified. We searched and summarized evidence from cohort-based and experimental studies on the issue of Nf1 and heart development in congenital heart diseases from various databases. Available evidence demonstrates a correlation between Nf1 and congenital heart diseases, mainly pulmonary valvar stenosis. The mechanism underlying this correlation may involve dysregulation of epithelial-mesenchymal transition (EMT). The Nf1 gene affects the EMT process via multiple pathways, including directly regulating the expression of EMT-related transcription factors and indirectly regulating the EMT process by regulating the MAPK pathway. This narrative review provides a comprehensive account of the Nf1 involvement in heart development and congenital cardiovascular diseases in terms of epidemiology and potential mechanisms. RAS signaling may contribute to congenital heart disease independently or in cooperation with other signaling pathways. Efficient management of both NF1 and cardiovascular disease patients would benefit from further research into these issues.
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Affiliation(s)
- Dun Wang
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
| | - Xue Wen
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
| | - Li-Li Xu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, People's Republic of China
| | - Qing-Xing Chen
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, People's Republic of China
| | - Tian-Xing Yan
- Central Laboratory, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
| | - Hai-Tao Xiao
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
| | - Xue-Wen Xu
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
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18
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Carcavilla A, Cambra A, Santomé JL, Seidel V, Cruz J, Alonso M, Pozo J, Valenzuela I, Guillén-Navarro E, Santos-Simarro F, González-Casado I, Rodríguez A, Medrano C, López-Siguero JP, Ezquieta B. Genotypic Findings in Noonan and Non-Noonan RASopathies and Patient Eligibility for Growth Hormone Treatment. J Clin Med 2023; 12:5003. [PMID: 37568403 PMCID: PMC10420167 DOI: 10.3390/jcm12155003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Molecular study has become an invaluable tool in the field of RASopathies. Treatment with recombinant human growth hormone is approved in Noonan syndrome but not in the other RASopathies. The aim of this study was to learn about the molecular base of a large cohort of patients with RASopathies, with particular emphasis on patients with pathogenic variants in genes other than PTPN11, and its potential impact on rGH treatment indication. We reviewed the clinical diagnosis and molecular findings in 451 patients with a genetically confirmed RASopathy. HRAS alterations were detected in only 2 out of 19 patients referred with a Costello syndrome suspicion, whereas pathogenic variants in RAF1 and SHOC2 were detected in 3 and 2, respectively. In 22 patients referred with a generic suspicion of RASopathy, including cardiofaciocutaneous syndrome, pathogenic alterations in classic Noonan syndrome genes (PTPN11, SOS1, RAF1, LZTR1, and RIT1) were found in 7 patients and pathogenic variants in genes associated with other RASopathies (HRAS, SHOC2, and PPPCB1) in 4. The correct nosological classification of patients with RASopathies is critical to decide whether they are candidates for treatment with rhGH. Our data illustrate the complexity of differential diagnosis in RASopathies, as well as the importance of genetic testing to guide the diagnostic orientation in these patients.
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Affiliation(s)
- Atilano Carcavilla
- Pediatric Endocrinology Department, Hospital Universitario La Paz, 28046 Madrid, Spain
- Multidisciplinary Unit for RASopathies, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Ana Cambra
- Molecular Diagnostics Laboratory, Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Gregorio Marañon Health Research Institute (IiSGM), 28009 Madrid, Spain
| | - José L. Santomé
- Molecular Diagnostics Laboratory, Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Gregorio Marañon Health Research Institute (IiSGM), 28009 Madrid, Spain
| | - Verónica Seidel
- Clinical Genetics Unit, Pediatrics Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
| | - Jaime Cruz
- Pediatrics Department, Hospital Universitario Doce de Octubre, 28041 Madrid, Spain
| | - Milagros Alonso
- Pediatrics Department, Hospital Ramón y Cajal, 28034 Madrid, Spain
| | - Jesús Pozo
- Pediatric Endocrinology Department, Hospital Universitario Niño Jesús, 28009 Madrid, Spain
| | - Irene Valenzuela
- Genetics Department, Hospital Universitario Vall D’Hebrón, 08035 Barcelona, Spain
| | | | - Fernando Santos-Simarro
- Multidisciplinary Unit for RASopathies, Hospital Universitario La Paz, 28046 Madrid, Spain
- Institute of Medical & Molecular Genetics, Hospital Universitario la Paz, 28046 Madrid, Spain
| | - Isabel González-Casado
- Pediatric Endocrinology Department, Hospital Universitario La Paz, 28046 Madrid, Spain
- Multidisciplinary Unit for RASopathies, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Amparo Rodríguez
- Gregorio Marañon Health Research Institute (IiSGM), 28009 Madrid, Spain
- Pediatric Endocrinology, Pediatrics Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
| | - Constancio Medrano
- Gregorio Marañon Health Research Institute (IiSGM), 28009 Madrid, Spain
- Pediatric Cardiology Department, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
| | - Juan Pedro López-Siguero
- Pediatric Endocrinology Department, Hospital Regional Universitario de Málaga, 29010 Málaga, Spain
| | - Begoña Ezquieta
- Molecular Diagnostics Laboratory, Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, 28007 Madrid, Spain
- Gregorio Marañon Health Research Institute (IiSGM), 28009 Madrid, Spain
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19
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Qu WZ, Wang L, Chen JJ, Wang Y. Raf kinase inhibitor protein combined with phosphorylated extracellular signal-regulated kinase offers valuable prognosis in gastrointestinal stromal tumor. World J Gastroenterol 2023; 29:4200-4213. [PMID: 37475847 PMCID: PMC10354573 DOI: 10.3748/wjg.v29.i26.4200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/20/2023] [Accepted: 06/02/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. Tyrosine kinase inhibitors, such as imatinib, have been used as first-line therapy for the treatment of GISTs. Although these drugs have achieved considerable efficacy in some patients, reports of resistance and recurrence have emerged. Extracellular signal-regulated kinase 1/2 (ERK1/2) protein, as a member of the mitogen-activated protein kinase (MAPK) family, is a core molecule of this signaling pathway. Nowadays, research reports on the important clinical and prognostic value of phosphorylated-ERK (P-ERK) and phosphorylated-MAPK/ERK kinase (P-MEK) proteins closely related to raf kinase inhibitor protein (RKIP) have gradually emerged in digestive tract tumors such as gastric cancer, colon cancer, and pancreatic cancer. However, literature on the expression of these downstream proteins combined with RKIP in GIST is scarce. This study will focus on this aspect and search for answers to the problem.
AIM To detect the expression of RKIP, P-ERK, and P-MEK protein in GIST and to analyze their relationship with clinicopathological characteristics and prognosis of this disease. Try to establish a new prognosis evaluation model using RKIP and P-ERK in combination with analysis and its prognosis evaluation efficacy.
METHODS The research object of our experiment was 66 pathologically diagnosed GIST patients with complete clinical and follow-up information. These patients received surgical treatment at China Medical University Affiliated Hospital from January 2015 to January 2020. Immunohistochemical method was used to detect the expression of RKIP, P-ERK, and P-MEK proteins in GIST tissue samples from these patients. Kaplan-Meier method was used to calculate the survival rate of 63 patients with complete follow-up data. A Nomogram was used to represent the new prognostic evaluation model. The Cox multivariate regression analysis was conducted separately for each set of risk evaluation factors, based on two risk classification systems [the new risk grade model vs the modified National Institutes of Health (NIH) 2008 risk classification system]. Receiver operating characteristic (ROC) curves were used for evaluating the accuracy and efficiency of the two prognostic evaluation systems.
RESULTS In GIST tissues, RKIP protein showed positive expression in the cytoplasm and cell membrane, appearing as brownish-yellow or brown granules. The expression of RKIP was related to GIST tumor size, NIH grade, and mucosal invasion. P-ERK protein exhibited heterogeneous distribution in GIST cells, mainly in the cytoplasm, with occasional presence in the nucleus, and appeared as brownish-yellow granules, and the expression of P-ERK protein was associated with GIST tumor size, mitotic count, mucosal invasion, and NIH grade. Meanwhile, RKIP protein expression was negatively correlated with P-ERK expression. The results in COX multivariate regression analysis showed that RKIP protein expression was not an independent risk factor for tumor prognosis. However, RKIP combined with P-ERK protein expression were identified as independent risk factors for prognosis with statistical significance. Furthermore, we establish a new prognosis evaluation model using RKIP and P-ERK in combination and obtained the nomogram of the new prognosis evaluation model. ROC curve analysis also showed that the new evaluation model had better prognostic performance than the modified NIH 2008 risk classification system.
CONCLUSION Our experimental results showed that the expression of RKIP and P-ERK proteins in GIST was associated with tumor size, NIH 2008 staging, and tumor invasion, and P-ERK expression was also related to mitotic count. The expression of the two proteins had a certain negative correlation. The combined expression of RKIP and P-ERK proteins can serve as an independent risk factor for predicting the prognosis of GIST patients. The new risk assessment model incorporating RKIP and P-ERK has superior evaluation efficacy and is worth further practical application to validate.
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Affiliation(s)
- Wen-Zhi Qu
- Department of General Surgery, The 4th Affiliated Hospital of China Medical University, Shenyang 110032, Liaoning Province, China
| | - Luan Wang
- Department of Emergency, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
| | - Juan-Juan Chen
- Department of Medical Service, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
| | - Yang Wang
- Department of General Surgery, The 4th Affiliated Hospital of China Medical University, Shenyang 110032, Liaoning Province, China
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20
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Suspitsin EN, Imyanitov EN. Hereditary Conditions Associated with Elevated Cancer Risk in Childhood. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:880-891. [PMID: 37751861 DOI: 10.1134/s0006297923070039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 09/28/2023]
Abstract
Received January, 31, 2023 Revised March, 16, 2023 Accepted March, 18, 2023 Widespread use of the next-generation sequencing (NGS) technologies revealed that a significant percentage of tumors in children develop as a part of monogenic hereditary diseases. Predisposition to the development of pediatric neoplasms is characteristic of a wide range of conditions including hereditary tumor syndromes, primary immunodeficiencies, RASopathies, and phakomatoses. The mechanisms of tumor molecular pathogenesis are diverse and include disturbances in signaling cascades, defects in DNA repair, chromatin remodeling, and microRNA processing. Timely diagnosis of tumor-associated syndromes is important for the proper choice of cancer treatment, genetic counseling of families, and development of the surveillance programs. The review describes the spectrum of neoplasms characteristic of the most common syndromes and molecular pathogenesis of these diseases.
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Affiliation(s)
- Evgeny N Suspitsin
- N. N. Petrov National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Saint Petersburg, 197758, Russia.
- St.-Petersburg State Pediatric Medical University, Saint Petersburg, 194100, Russia
| | - Evgeny N Imyanitov
- N. N. Petrov National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Saint Petersburg, 197758, Russia
- St.-Petersburg State Pediatric Medical University, Saint Petersburg, 194100, Russia
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21
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Dimitri P. Precision diagnostics in children. CAMBRIDGE PRISMS. PRECISION MEDICINE 2023; 1:e17. [PMID: 38550930 PMCID: PMC10953773 DOI: 10.1017/pcm.2023.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 01/05/2023] [Accepted: 01/13/2023] [Indexed: 11/06/2024]
Abstract
Medical practice is transforming from a reactive to a pro-active and preventive discipline that is underpinned by precision medicine. The advances in technologies in such fields as genomics, proteomics, metabolomics, transcriptomics and artificial intelligence have resulted in a paradigm shift in our understanding of specific diseases in childhood, greatly enhanced by our ability to combine data from changes within cells to the impact of environmental and population changes. Diseases in children have been reclassified as we understand more about their genomic origin and their evolution. Genomic discoveries, additional 'omics' data and advances such as optical genome mapping have driven rapid improvements in the precision and speed of diagnoses of diseases in children and are now being incorporated into newborn screening, have improved targeted therapies in childhood and have supported the development of predictive biomarkers to assess therapeutic impact and determine prognosis in congenital and acquired diseases of childhood. New medical device technologies are facilitating data capture at a population level to support higher diagnostic accuracy and tailored therapies in children according to predicted population outcome, and digital ecosystems now tailor therapies and provide support for their specific needs. By capturing biological and environmental data as early as possible in childhood, we can understand factors that predict disease or maintain health and track changes across a more extensive longitudinal path. Data from multiple health and external sources over long-time periods starting from birth or even in the in utero environment will provide further clarity about how to sustain health and prevent or predict disease. In this respect, we will not only use data to diagnose disease, but precision diagnostics will aid the 'diagnosis of good health'. The principle of 'start early and change more' will thus underpin the value of applying a personalised medicine approach early in life.
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Affiliation(s)
- Paul Dimitri
- Department of Paediatric Endocrinology, Sheffield Children’s NHS Foundation Trust, Sheffield, UK
- The College of Health, Wellbeing and Life Sciences, Sheffield Hallam University, Sheffield, UK
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22
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Brown W, Wesalo J, Tsang M, Deiters A. Engineering Small Molecule Switches of Protein Function in Zebrafish Embryos. J Am Chem Soc 2023; 145:2395-2403. [PMID: 36662675 DOI: 10.1021/jacs.2c11366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Precise temporally regulated protein function directs the highly complex processes that make up embryo development. The zebrafish embryo is an excellent model organism to study development, and conditional control over enzymatic activity is desirable to target chemical intervention to specific developmental events and to investigate biological mechanisms. Surprisingly few, generally applicable small molecule switches of protein function exist in zebrafish. Genetic code expansion allows for site-specific incorporation of unnatural amino acids into proteins that contain caging groups that are removed through addition of small molecule triggers such as phosphines or tetrazines. This broadly applicable control of protein function was applied to activate several enzymes, including a GTPase and a protease, with temporal precision in zebrafish embryos. Simple addition of the small molecule to the media produces robust and tunable protein activation, which was used to gain insight into the development of a congenital heart defect from a RASopathy mutant of NRAS and to control DNA and protein cleavage events catalyzed by a viral recombinase and a viral protease, respectively.
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Affiliation(s)
- Wes Brown
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Joshua Wesalo
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Michael Tsang
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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23
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Norcross RG, Abdelmoti L, Rouchka EC, Andreeva K, Tussey O, Landestoy D, Galperin E. Shoc2 controls ERK1/2-driven neural crest development by balancing components of the extracellular matrix. Dev Biol 2022; 492:156-171. [PMID: 36265687 PMCID: PMC10019579 DOI: 10.1016/j.ydbio.2022.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/29/2022] [Accepted: 10/10/2022] [Indexed: 02/02/2023]
Abstract
The extracellular signal-regulated kinase (ERK1/2) pathway is essential in embryonic development. The scaffold protein Shoc2 is a critical modulator of ERK1/2 signals, and mutations in the shoc2 gene lead to the human developmental disease known as Noonan-like syndrome with loose anagen hair (NSLH). The loss of Shoc2 and the shoc2 NSLH-causing mutations affect the tissues of neural crest (NC) origin. In this study, we utilized the zebrafish model to dissect the role of Shoc2-ERK1/2 signals in the development of NC. These studies established that the loss of Shoc2 significantly altered the expression of transcription factors regulating the specification and differentiation of NC cells. Using comparative transcriptome analysis of NC-derived cells from shoc2 CRISPR/Cas9 mutant larvae, we found that Shoc2-mediated signals regulate gene programs at several levels, including expression of genes coding for the proteins of extracellular matrix (ECM) and ECM regulators. Together, our results demonstrate that Shoc2 is an essential regulator of NC development. This study also indicates that disbalance in the turnover of the ECM may lead to the abnormalities found in NSLH patients.
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Affiliation(s)
- Rebecca G Norcross
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA
| | - Lina Abdelmoti
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA
| | - Eric C Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, 40292, USA; KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY, 40292, USA
| | - Kalina Andreeva
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, KY, 40292, USA; Department of Neuroscience Training, University of Louisville, Louisville, KY, 40292, USA; Department of Genetics, Stanford University, Palo Alto, CA, 94304, USA
| | - Olivia Tussey
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA
| | - Daileen Landestoy
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA
| | - Emilia Galperin
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, 40536, USA.
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24
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Perafan-Valdes L, Giraldo-Ocampo S, Lores J, Pachajoa H. Neurofibromatosis Type 1 and Hypospadias in a Male 46, XY with a Mutation in the NF1 Gene and a Mutation in NR5A1. Pharmgenomics Pers Med 2022; 15:873-878. [PMCID: PMC9617560 DOI: 10.2147/pgpm.s380796] [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: 07/01/2022] [Accepted: 09/22/2022] [Indexed: 11/23/2022] Open
Abstract
Neurofibromatosis type 1 is one of the most common genetic autosomal dominant disorders described, with a prevalence of 1 in 2000 to 1 in 3000 individuals. It is characterized by skin, nerves, and bone abnormalities. Non-related to NF1, hypospadias is a displacement in the urethral opening which in the majority of patients has an idiopathic cause. Here, we describe a patient with neurofibromatosis type 1, hypospadias, and unilateral cryptorchidism. The heterozygous variants c.6789_6792delTTAC, p.(Tyr2264Thrfs*5) and c.140A>G, p.(Tyr47Cys) were found in the NF1 and NR5A1 genes, respectively. This case contributes to the phenotypical characterization of patients with NF1 but also with hypospadias caused by a mutation in the NR5A1 gene, which usually leads to severe sex disorders.
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Affiliation(s)
- Lina Perafan-Valdes
- Universidad Libre, Programa de Maestría en Epidemiología, Cali, Colombia,Fundación Valle del Lili, Genetics Division, Cali, Colombia
| | | | - Juliana Lores
- Fundación Valle del Lili, Genetics Division, Cali, Colombia
| | - Harry Pachajoa
- Fundación Valle del Lili, Genetics Division, Cali, Colombia,Universidad Icesi, Centro de Investigaciones en Anomalías Congénitas y Enfermedades Raras (CIACER), Cali, Colombia,Correspondence: Harry Pachajoa, Fundación Valle del Lili, Genetics Division, Carrera 98 # 18-49, Cali, Colombia, Tel +57 5552334 ext 7653, Email
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25
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Abstract
Signaling via extracellular regulated kinase 1/2 (ERK1/2) and p90 ribosomal S6 kinase (RSK), a downstream effector, mediates numerous processes. For example, ERK1/2-RSK signaling is essential for estrogen homeostasis in the mammary gland and uterus to maintain physiological responsiveness. This review will focus on the coordination of ERK1/2-RSK2 and estrogen signaling through estrogen receptor alpha (ERα). The interrelationship and the feedback mechanisms between these pathways occurs at the level of transcription, translation, and posttranslational modification. Identifying how ERK1/2-RSK2 and estrogen signaling cooperate in homeostasis and disease may lead to novel therapeutic approaches in estrogen-dependent disorders.
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Affiliation(s)
- Deborah A Lannigan
- Correspondence: Deborah A. Lannigan, PhD, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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26
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Hauseman ZJ, Fodor M, Dhembi A, Viscomi J, Egli D, Bleu M, Katz S, Park E, Jang DM, Porter KA, Meili F, Guo H, Kerr G, Mollé S, Velez-Vega C, Beyer KS, Galli GG, Maira SM, Stams T, Clark K, Eck MJ, Tordella L, Thoma CR, King DA. Structure of the MRAS-SHOC2-PP1C phosphatase complex. Nature 2022; 609:416-423. [PMID: 35830882 PMCID: PMC9452295 DOI: 10.1038/s41586-022-05086-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/07/2022] [Indexed: 11/09/2022]
Abstract
RAS-MAPK signalling is fundamental for cell proliferation and is altered in most human cancers1-3. However, our mechanistic understanding of how RAS signals through RAF is still incomplete. Although studies revealed snapshots for autoinhibited and active RAF-MEK1-14-3-3 complexes4, the intermediate steps that lead to RAF activation remain unclear. The MRAS-SHOC2-PP1C holophosphatase dephosphorylates RAF at serine 259, resulting in the partial displacement of 14-3-3 and RAF-RAS association3,5,6. MRAS, SHOC2 and PP1C are mutated in rasopathies-developmental syndromes caused by aberrant MAPK pathway activation6-14-and SHOC2 itself has emerged as potential target in receptor tyrosine kinase (RTK)-RAS-driven tumours15-18. Despite its importance, structural understanding of the SHOC2 holophosphatase is lacking. Here we determine, using X-ray crystallography, the structure of the MRAS-SHOC2-PP1C complex. SHOC2 bridges PP1C and MRAS through its concave surface and enables reciprocal interactions between all three subunits. Biophysical characterization indicates a cooperative assembly driven by the MRAS GTP-bound active state, an observation that is extendible to other RAS isoforms. Our findings support the concept of a RAS-driven and multi-molecular model for RAF activation in which individual RAS-GTP molecules recruit RAF-14-3-3 and SHOC2-PP1C to produce downstream pathway activation. Importantly, we find that rasopathy and cancer mutations reside at protein-protein interfaces within the holophosphatase, resulting in enhanced affinities and function. Collectively, our findings shed light on a fundamental mechanism of RAS biology and on mechanisms of clinically observed enhanced RAS-MAPK signalling, therefore providing the structural basis for therapeutic interventions.
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Affiliation(s)
| | - Michelle Fodor
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Anxhela Dhembi
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Jessica Viscomi
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - David Egli
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Melusine Bleu
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Stephanie Katz
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Eunyoung Park
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dong Man Jang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Fabian Meili
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Hongqiu Guo
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Grainne Kerr
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Sandra Mollé
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Kim S Beyer
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Giorgio G Galli
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Travis Stams
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Kirk Clark
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Michael J Eck
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Luca Tordella
- Novartis Institutes for BioMedical Research, Basel, Switzerland.
| | - Claudio R Thoma
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
| | - Daniel A King
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
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Stagi S, Ferrari V, Ferrari M, Priolo M, Tartaglia M. Inside the Noonan "universe": Literature review on growth, GH/IGF axis and rhGH treatment: Facts and concerns. Front Endocrinol (Lausanne) 2022; 13:951331. [PMID: 36060964 PMCID: PMC9434367 DOI: 10.3389/fendo.2022.951331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/18/2022] [Indexed: 12/21/2022] Open
Abstract
Noonan syndrome (NS) is a disorder characterized by a typical facial gestalt, congenital heart defects, variable cognitive deficits, skeletal defects, and short stature. NS is caused by germline pathogenic variants in genes coding proteins with a role in the RAS/mitogen-activated protein kinase signaling pathway, and it is typically associated with substantial genetic and clinical complexity and variability. Short stature is a cardinal feature in NS, with evidence indicating that growth hormone (GH) deficiency, partial GH insensitivity, and altered response to insulin-like growth factor I (IGF-1) are contributing events for growth failure in these patients. Decreased IGF-I, together with low/normal responses to GH pharmacological provocation tests, indicating a variable presence of GH deficiency/resistance, in particular in subjects with pathogenic PTPN11 variants, are frequently reported. Nonetheless, short- and long-term studies have demonstrated a consistent and significant increase in height velocity (HV) in NS children and adolescents treated with recombinant human GH (rhGH). While the overall experience with rhGH treatment in NS patients with short stature is reassuring, it is difficult to systematically compare published data due to heterogeneous protocols, potential enrolment bias, the small size of cohorts in many studies, different cohort selection criteria and varying durations of therapy. Furthermore, in most studies, the genetic information is lacking. NS is associated with a higher risk of benign and malignant proliferative disorders and hypertrophic cardiomyopathy, and rhGH treatment may further increase risk in these patients, especially as dosages vary widely. Herein we provide an updated review of aspects related to growth, altered function of the GH/IGF axis and cell response to GH/IGF stimulation, rhGH treatment and its possible adverse events. Given the clinical variability and genetic heterogeneity of NS, treatment with rhGH should be personalized and a conservative approach with judicious surveillance is recommended. Depending on the genotype, an individualized follow-up and close monitoring during rhGH treatments, also focusing on screening for neoplasms, should be considered.
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Affiliation(s)
- Stefano Stagi
- Department of Health Sciences, University of Florence, Anna Meyer Children’s University Hospital, Florence, Italy
| | - Vittorio Ferrari
- Department of Health Sciences, University of Florence, Anna Meyer Children’s University Hospital, Florence, Italy
| | - Marta Ferrari
- Department of Health Sciences, University of Florence, Anna Meyer Children’s University Hospital, Florence, Italy
| | - Manuela Priolo
- Medical Genetics Unit, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, Reggio Calabria, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
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Abstract
Immunity could be viewed as the common factor in neurodevelopmental disorders and cancer. The immune and nervous systems coevolve as the embryo develops. Immunity can release cytokines that activate MAPK signaling in neural cells. In specific embryonic brain cell types, dysregulated signaling that results from germline or embryonic mutations can promote changes in chromatin organization and gene accessibility, and thus expression levels of essential genes in neurodevelopment. In cancer, dysregulated signaling can emerge from sporadic somatic mutations during human life. Neurodevelopmental disorders and cancer share similarities. In neurodevelopmental disorders, immunity, and cancer, there appears an almost invariable involvement of small GTPases (e.g., Ras, RhoA, and Rac) and their pathways. TLRs, IL-1, GIT1, and FGFR signaling pathways, all can be dysregulated in neurodevelopmental disorders and cancer. Although there are signaling similarities, decisive differentiating factors are timing windows, and cell type specific perturbation levels, pointing to chromatin reorganization. Finally, we discuss drug discovery.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Corresponding author
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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Watt SM, Hua P, Roberts I. Increasing Complexity of Molecular Landscapes in Human Hematopoietic Stem and Progenitor Cells during Development and Aging. Int J Mol Sci 2022; 23:3675. [PMID: 35409034 PMCID: PMC8999121 DOI: 10.3390/ijms23073675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 02/05/2023] Open
Abstract
The past five decades have seen significant progress in our understanding of human hematopoiesis. This has in part been due to the unprecedented development of advanced technologies, which have allowed the identification and characterization of rare subsets of human hematopoietic stem and progenitor cells and their lineage trajectories from embryonic through to adult life. Additionally, surrogate in vitro and in vivo models, although not fully recapitulating human hematopoiesis, have spurred on these scientific advances. These approaches have heightened our knowledge of hematological disorders and diseases and have led to their improved diagnosis and therapies. Here, we review human hematopoiesis at each end of the age spectrum, during embryonic and fetal development and on aging, providing exemplars of recent progress in deciphering the increasingly complex cellular and molecular hematopoietic landscapes in health and disease. This review concludes by highlighting links between chronic inflammation and metabolic and epigenetic changes associated with aging and in the development of clonal hematopoiesis.
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Affiliation(s)
- Suzanne M. Watt
- Stem Cell Research, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9BQ, UK
- Myeloma Research Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, North Terrace, Adelaide 5005, Australia
- Cancer Program, Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide 5001, Australia
| | - Peng Hua
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China;
| | - Irene Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, and NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK;
- Department of Paediatrics and NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford OX3 9DU, UK
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Harnessing RKIP to Combat Heart Disease and Cancer. Cancers (Basel) 2022; 14:cancers14040867. [PMID: 35205615 PMCID: PMC8870036 DOI: 10.3390/cancers14040867] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 02/06/2023] Open
Abstract
Cancer and heart disease are leading causes of morbidity and mortality worldwide. These diseases have common risk factors, common molecular signaling pathways that are central to their pathogenesis, and even some disease phenotypes that are interdependent. Thus, a detailed understanding of common regulators is critical for the development of new and synergistic therapeutic strategies. The Raf kinase inhibitory protein (RKIP) is a regulator of the cellular kinome that functions to maintain cellular robustness and prevent the progression of diseases including heart disease and cancer. Two of the key signaling pathways controlled by RKIP are the β-adrenergic receptor (βAR) signaling to protein kinase A (PKA), particularly in the heart, and the MAP kinase cascade Raf/MEK/ERK1/2 that regulates multiple diseases. The goal of this review is to discuss how we can leverage RKIP to suppress cancer without incurring deleterious effects on the heart. Specifically, we discuss: (1) How RKIP functions to either suppress or activate βAR (PKA) and ERK1/2 signaling; (2) How we can prevent cancer-promoting kinase signaling while at the same time avoiding cardiotoxicity.
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Nussinov R, Tsai CJ, Jang H. How can same-gene mutations promote both cancer and developmental disorders? SCIENCE ADVANCES 2022; 8:eabm2059. [PMID: 35030014 PMCID: PMC8759737 DOI: 10.1126/sciadv.abm2059] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/22/2021] [Indexed: 05/05/2023]
Abstract
The question of how same-gene mutations can drive both cancer and neurodevelopmental disorders has been puzzling. It has also been puzzling why those with neurodevelopmental disorders have a high risk of cancer. Ras, MEK, PI3K, PTEN, and SHP2 are among the oncogenic proteins that can harbor mutations that encode diseases other than cancer. Understanding why some of their mutations can promote cancer, whereas others promote neurodevelopmental diseases, and why even the same mutations may promote both phenotypes, has important clinical ramifications. Here, we review the literature and address these tantalizing questions. We propose that cell type–specific expression of the mutant protein, and of other proteins in the respective pathway, timing of activation (during embryonic development or sporadic emergence), and the absolute number of molecules that the mutations activate, alone or in combination, are pivotal in determining the pathological phenotypes—cancer and (or) developmental disorders.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
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Szczawińska-Popłonyk A, Popłonyk N, Niedziela M, Sowińska-Seidler A, Sztromwasser P, Jamsheer A, Obara-Moszyńska M. Case report: The cardio-facio-cutaneous syndrome due to a novel germline mutation in MAP2K1: A multifaceted disease with immunodeficiency and short stature. Front Pediatr 2022; 10:990111. [PMID: 36313893 PMCID: PMC9614356 DOI: 10.3389/fped.2022.990111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/26/2022] [Indexed: 11/28/2022] Open
Abstract
Cardio-facio-cutaneous syndrome (CFCS) belongs to the group of RASopathies, clinical disorders defined by disruptions in the RAS/MAPK signaling pathway. It is caused by heterozygous gain-of-function germline mutations in genes encoding protein kinases: BRAF, MAP2K1 (MEK1), MAP2K2 (MEK2), and in the GTPase-encoding gene KRAS. CFCS is characterized by craniofacial dysmorphic features, congenital heart defects, severe malnutrition, proportionate short stature, anomalies within the structure of skin and hair, and psychomotor disability. The pathophysiology of growth impairment is multifactorial with feeding difficulties, growth hormone deficiency, and insensitivity. Immunodeficiency has not been hitherto reported as an integral part of CFCS yet an increased activation of the RAS/MAPK signaling pathway may contribute to explaining the causal relationship between RASopathy and the dysfunctions within the B and T lymph cell compartments resulting in a deficiency in T cell costimulation and B cell maturation with impaired class switch recombination, somatic hypermutation, and high-affinity antibody production. We report on a boy born prematurely at 32 WGA, with the perinatal period complicated by pneumonia, respiratory distress syndrome, and valvular pulmonary stenosis. The boy suffered from recurrent pneumonia, obstructive bronchitis, sepsis, urinary tract infection, and recurrent fevers. He presented with severe hypotrophy, psychomotor disability, short stature, craniofacial dysmorphism, dental hypoplasia, sparse hair, and cryptorchidism. Whole genome sequencing showed a novel heterozygous pathogenic germline missense variant: c.364A > G; p.Asn122Asp in the MAP2K1 gene, supporting the diagnosis of CFCS. The immunological workup revealed hypogammaglobulinemia, IgG subclass, and specific antibody deficiency accompanied by decreased numbers of T helper cells and naive and memory B cells. Replacement immunoglobulin therapy with timely antibiotic prophylaxis were instituted. At the age of six years, growth hormone deficiency was diagnosed and the rGH therapy was started. The ever-increasing progress in genetic studies contributes to establishing the definitive CFCS diagnosis and sheds the light on the interrelated genotype-phenotype heterogeneity of RASopathies. Herein, we add new phenotypic features of predominating humoral immunodeficiency to the symptomatology of CFCS with a novel mutation in MAP2K1. While CFCS is a multifaceted disease, increased pediatricians' awareness is needed to prevent the delay in diagnostics and therapeutic interventions.
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Affiliation(s)
- Aleksandra Szczawińska-Popłonyk
- Department of Pediatric Pneumonology, Allergy and Clinical Immunology, Institute of Pediatrics, Poznań University of Medical Sciences, Poznań, Poland
| | - Natalia Popłonyk
- Student Scientific Society for Pediatric Endocrinology, Poznań University of Medical Sciences, Poznań, Poland
| | - Marek Niedziela
- Department of Pediatric Endocrinology and Rheumatology, Institute of Pediatrics, Poznań University of Medical Sciences, Poznań, Poland
| | - Anna Sowińska-Seidler
- Department of Medical Genetics, Poznań University of Medical Sciences, Poznań, Poland
| | - Paweł Sztromwasser
- Department of Biostatistics and Translational Medicine, Medical University of Łódź, Łódź, Poland.,MNM Diagnostics, Poznań, Poland
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznań University of Medical Sciences, Poznań, Poland
| | - Monika Obara-Moszyńska
- Department of Pediatric Endocrinology and Rheumatology, Institute of Pediatrics, Poznań University of Medical Sciences, Poznań, Poland
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ERAS, a Member of the Ras Superfamily, Acts as an Oncoprotein in the Mammary Gland. Cancers (Basel) 2021; 13:cancers13215588. [PMID: 34771750 PMCID: PMC8582886 DOI: 10.3390/cancers13215588] [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: 10/22/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The genes of the RAS family are among the group of genes most frequently mutated in human cancer. ERAS is a relatively unknown gene of this family. Although ERAS is overexpressed in some tumoral samples and in several cancer cell lines of human origin, it is not known if its expression drives tumor formation or if, alternatively, its expression is a secondary event in tumoral transformation. In this report, in order to clarify the role of ERAS in mammary tumorigenesis, we studied transgenic mice expressing ERAS in myoepithelial cells of mammary and other exocrine glands and in basal cells of stratified epithelia. These mice displayed an altered development and function of the mammary glands, and suffered high-frequency tumoral lesions in the mammary glands resembling a rare human breast tumor named malignant adenomyoepithelioma. Our results clearly demonstrate that ERAS is a true oncogene able to produce mammary tumors when inappropriately expressed. Abstract ERAS is a relatively uncharacterized gene of the Ras superfamily. It is expressed in ES cells and in the first stages of embryonic development; later on, it is silenced in the majority of cell types and tissues. Although there are several reports showing ERAS expression in tumoral cell lines and human tumor samples, it is unknown if ERAS deregulated expression is enough to drive tumor development. In this report, we have generated transgenic mice expressing ERAS in myoepithelial basal cells of the mammary gland and in basal cells of stratified epithelia. In spite of the low level of ERAS expression, these transgenic mice showed phenotypic alterations resembling overgrowth syndromes caused by the activation of the AKT-PI3K pathway. In addition, their mammary glands present developmental and functional disabilities accompanied by morphological and biochemical alterations in the myoepithelial cells. These mice suffer from tumoral transformation in the mammary glands with high incidence. These mammary tumors resemble, both histologically and by the expression of differentiation markers, malignant adenomyoepitheliomas. In sum, our results highlight the importance of ERAS silencing in adult tissues and define a truly oncogenic role for ERAS in mammary gland cells when inappropriately expressed.
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Kattner AA. We refuse to die - T cells causing havoc. Biomed J 2021; 44:377-382. [PMID: 34508914 PMCID: PMC8514847 DOI: 10.1016/j.bj.2021.08.012] [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] [Received: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 10/28/2022] Open
Abstract
This issue of the Biomedical Journal offers insights into the origin and consequences of different lymphoproliferative disorders and autoimmunity. Furthermore we learn about RASopathies, a group of congenital disorders that occur rather frequently. Then the current ELISA assays for measuring antibody avidity are critically examined, the relationship between female sex steroid hormones and cardiovascular disease is explored, and an assessment of persistent diarrhea as a leading cause of child death in India is performed. Additionally, there are several articles about COVID-19, presenting its connection to neutrophil recruitment and acute respiratory distress syndrome, as well as its relation to changes in the vascular glycocalyx. A COVID-19 case study from the emergency room is presented. We are also introduced to novel treatment approaches against COVID-19 like the construction of peptide-based vaccines, or targeting the respiratory tract microbiome. Finally, there is an assessment about how prepared medical students at a Taiwan University feel for independent practice, and another article about the treatment of intravascular large B cell lymphoma in a Taiwanese institution. Lastly, we discover possible surgery techniques in the case of external auditory canal osteoma.
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Abstract
This special issue contains four review articles that describe advances in analysis of mutations responsible for the autoimmune lymphoproliferative syndrome (ALPS). This disease is triggered by a family of mutations in genes involved in the extrinsic apoptotic pathway such as FAS, FASL and CASP10. Advances in sequencing technology have enabled extended genetic testing of patients with various defects in alternative biological have pathways that can cause ALPS-like syndromes. Various gene mutations were identified which affect the CTLA-4 immune checkpoint, the STAT3 pathway and the RAS/MAPK pathway. Tips gleaned from analyses of the different gene mutations involved in ALPS and ALPS-like syndromes are contributing to a better understanding of their functional consequences. Genetic diagnoses of the disease should help us to identify specific therapeutic targets and design personalized treatment for each patient.
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