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Maryami F, Davoudi-Dehaghani E, Khalesi N, Rismani E, Rahimi H, Talebi S, Zeinali S. Identification and characterization of the largest deletion in the PCCA gene causing severe acute early-onset form of propionic acidemia. Mol Genet Genomics 2023; 298:905-917. [PMID: 37131081 DOI: 10.1007/s00438-023-02023-3] [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: 06/29/2022] [Accepted: 04/16/2023] [Indexed: 05/04/2023]
Abstract
Whole-exome sequencing (WES) is an excellent method for the diagnosis of diseases of uncertain or heterogeneous genetic origin. However, it has limitations for detecting structural variations such as InDels, which the bioinformatics analyzers must be aware of. This study aimed at using WES to evaluate the genetic cause of the metabolic crisis in a 3-day-old neonate admitted to the neonatal intensive care unit (NICU) and deceased after a few days. Tandem mass spectrometry (MS/MS) showed a significant increase in propionyl carnitine (C3), proposing methylmalonic acidemia (MMA) or propionic acidemia (PA). WES demonstrated a homozygous missense variant in exon 4 of the BTD gene (NM_000060.4(BTD):c.1330G > C), responsible for partial biotinidase deficiency. Segregation analysis of the BTD variant revealed the homozygous status of the asymptomatic mother. Furthermore, observation of the bam file, around genes responsible for PA or MMA, by Integrative Genomics Viewer (IGV) software displayed a homozygous large deletion in the PCCA gene. Comprehensive confirmatory studies identified and segregated a novel outframe deletion of 217,877 bp length, "NG_008768.1:g.185211_403087delinsTA", extended from intron 11 to 21 of the PCCA, inducing a premature termination codon and activation of nonsense-mediated mRNA decay (NMD). Homology modeling of the mutant PCCA demonstrated eliminating the protein's active site and critical functional domains. Thereupon, this novel variant is suggested as the largest deletion in the PCCA gene, causing an acute early-onset PA. These results could expand the PCCA variants spectrum, and improve the existing knowledge on the molecular basis of PA, as well as provide new evidence of pathogenicity of the variant (NM_000060.4(BTD):c.1330G > C.
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Affiliation(s)
- Fereshteh Maryami
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Elham Davoudi-Dehaghani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Nasrin Khalesi
- Department of Pediatrics and Neonatal Intensive Care Unit, Ali-Asghar Children's Hospital, Iran University of Medical Sciences, Shahid Vahid Dastgerdi Street, Modarres Highway, Tehran, Iran.
| | - Elham Rismani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
| | - Hamzeh Rahimi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran
- Texas Biomedical Research Center, San Antonio, USA
| | - Saeed Talebi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Department of Medical Genetics, Ali-Asghar Children's Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran, Iran.
- Medical Genetics Lab, Kawsar Human Genetics Research Center, No. 41 Majlesi St., ValiAsr St., 1595645513, Tehran, Iran.
- Iranian Molecular Medicine Network, Pasteur Institute of Iran, Pasteur St, Tehran, Iran.
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Shotelersuk V, Tongsima S, Pithukpakorn M, Eu‐ahsunthornwattana J, Mahasirimongkol S. Precision medicine in Thailand. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:245-253. [DOI: 10.1002/ajmg.c.31694] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of MedicineChulalongkorn University Bangkok Thailand
- Excellence Center for Medical GeneticsKing Chulalongkorn Memorial Hospital, the Thai Red Cross Society Bangkok Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and BiotechnologyNational Science and Technology Development Agency Pathum Thani Thailand
| | - Manop Pithukpakorn
- Division of Medical Genetics, Department of MedicineFaculty of Medicine Siriraj Hospital, Mahidol University Bangkok Thailand
- Siriraj Center of Research Excellence in Precision MedicineFaculty of Medicine Siriraj Hospital, Mahidol University Bangkok Thailand
| | - Jakris Eu‐ahsunthornwattana
- Department of Community MedicineFaculty of Medicine Ramathibodi Hospital, Mahidol University Bangkok Thailand
- Division of Medical Genetics and Molecular Medicine, Department of Internal Medicine, Faculty of Medicine Ramathibodi HospitalMahidol University Bangkok Thailand
| | - Surakameth Mahasirimongkol
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical SciencesMinistry of Public Health Nonthaburi Thailand
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Abstract
PURPOSE OF REVIEW Recent clinical studies and management guidelines for the treatment of the organic acidopathies methylmalonic acidemia (MMA) and propionic acidemia address the scope of interventions to maximize health and quality of life. Unfortunately, these disorders continue to cause significant morbidity and mortality due to acute and chronic systemic and end-organ injury. RECENT FINDINGS Dietary management with medical foods has been a mainstay of therapy for decades, yet well controlled patients can manifest growth, development, cardiac, ophthalmological, renal, and neurological complications. Patients with organic acidopathies suffer metabolic brain injury that targets specific regions of the basal ganglia in a distinctive pattern, and these injuries may occur even with optimal management during metabolic stress. Liver transplantation has improved quality of life and metabolic stability, yet transplantation in this population does not entirely prevent brain injury or the development of optic neuropathy and cardiac disease. SUMMARY Management guidelines should identify necessary screening for patients with methylmalonic acidemia and propionic acidemia, and improve anticipatory management of progressive end-organ disease. Liver transplantation improves overall metabolic control, but injury to nonregenerative tissues may not be mitigated. Continued use of medical foods in these patients requires prospective studies to demonstrate evidence of benefit in a controlled manner.
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