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Mehvari S, Karimian Fathi N, Saki S, Asadnezhad M, Arzhangi S, Ghodratpour F, Mohseni M, Zare Ashrafi F, Sadeghian S, Boroumand M, Shokohizadeh F, Rostami E, Boroumand R, Najafipour R, Malekzadeh R, Riazalhosseini Y, Akbari M, Lathrop M, Najmabadi H, Hosseini K, Kahrizi K. Contribution of genetic variants in the development of familial premature coronary artery disease in a cohort of cardiac patients. Clin Genet 2024; 105:611-619. [PMID: 38308583 DOI: 10.1111/cge.14491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/18/2024] [Indexed: 02/05/2024]
Abstract
Coronary artery disease (CAD), the most prevalent cardiovascular disease, is the leading cause of death worldwide. Heritable factors play a significant role in the pathogenesis of CAD. It has been proposed that approximately one-third of patients with CAD have a positive family history, and individuals with such history are at ~1.5-fold increased risk of CAD in their lifespans. Accordingly, the long-recognized familial clustering of CAD is a strong risk factor for this disease. Our study aimed to identify candidate genetic variants contributing to CAD by studying a cohort of 60 large Iranian families with at least two members in different generations afflicted with premature CAD (PCAD), defined as established disease at ≤45 years in men and ≤55 years in women. Exome sequencing was performed for a subset of the affected individuals, followed by prioritization and Sanger sequencing of candidate variants in all available family members. Subsequently, apparently healthy carriers of potential risk variants underwent coronary computed tomography angiography (CCTA), followed by co-segregation analysis of the combined data. Putative causal variants were identified in seven genes, ABCG8, CD36, CYP27A1, PIK3C2G, RASSF9, RYR2, and ZFYVE21, co-segregating with familial PCAD in seven unrelated families. Among these, PIK3C2G, RASSF9, and ZFYVE21 are novel candidate CAD susceptibility genes. Our findings indicate that rare variants in genes identified in this study are involved in CAD development.
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Affiliation(s)
- Sepideh Mehvari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Nahid Karimian Fathi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sara Saki
- Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Asadnezhad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Ghodratpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Saeed Sadeghian
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadali Boroumand
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Shokohizadeh
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Elham Rostami
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Rahnama Boroumand
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Najafipour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Malekzadeh
- Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mohammadreza Akbari
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada
| | | | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kaveh Hosseini
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- McGill Genome Centre, Montreal, Quebec, Canada
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Alavi S, Mohammadimoghaddam S, Najmabadi H, Maghsoudlou S. The First Iranian Case of Unstable Hemoglobin Santa Ana. Hemoglobin 2024; 48:125-128. [PMID: 38500334 DOI: 10.1080/03630269.2024.2330554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/08/2024] [Indexed: 03/20/2024]
Abstract
In this report, we describe a 6-year-old girl with a medical history of pallor, mild icterus, anemia, blood transfusion and abnormal hemoglobin variant analysis on capillary electrophoresis. She was referred for further analysis. DNA sequencing of the proband revealed a de novo mutation in Codon 88 (CTG > CCG) of the β-globin gene (HBB: c.266T > C) in a heterozygous state compatible with hemoglobin Santa Ana, an unstable hemoglobin. This is the first case of Hb Santa Ana from Iran associated with moderate to severe anemia who underwent splenectomy with clinical improvement.
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Affiliation(s)
- Samin Alavi
- Pediatric Congenital Hematologic Disorders Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soha Mohammadimoghaddam
- Pediatric Congenital Hematologic Disorders Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Department of Genetics, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sina Maghsoudlou
- Department of Computer Science and Software Engineering, Concordia University, Montreal, QC, Canada
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Abolhassani A, Fattahi Z, Beheshtian M, Fadaee M, Vazehan R, Ahangari F, Dehdahsi S, Faraji Zonooz M, Parsimehr E, Kalhor Z, Peymani F, Mozaffarpour Nouri M, Babanejad M, Noudehi K, Fatehi F, Zamanian Najafabadi S, Afroozan F, Yazdan H, Bozorgmehr B, Azarkeivan A, Sadat Mahdavi S, Nikuei P, Fatehi F, Jamali P, Ashrafi MR, Karimzadeh P, Habibi H, Kahrizi K, Nafissi S, Kariminejad A, Najmabadi H. Clinical application of next generation sequencing for Mendelian disease diagnosis in the Iranian population. NPJ Genom Med 2024; 9:12. [PMID: 38374194 PMCID: PMC10876633 DOI: 10.1038/s41525-024-00393-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 01/29/2024] [Indexed: 02/21/2024] Open
Abstract
Next-generation sequencing (NGS) has been proven to be one of the most powerful diagnostic tools for rare Mendelian disorders. Several studies on the clinical application of NGS in unselected cohorts of Middle Eastern patients have reported a high diagnostic yield of up to 48%, correlated with a high level of consanguinity in these populations. We evaluated the diagnostic utility of NGS-based testing across different clinical indications in 1436 patients from Iran, representing the first study of its kind in this highly consanguineous population. A total of 1075 exome sequencing and 361 targeted gene panel sequencing were performed over 8 years at a single clinical genetics laboratory, with the majority of cases tested as proband-only (91.6%). The overall diagnostic rate was 46.7%, ranging from 24% in patients with an abnormality of prenatal development to over 67% in patients with an abnormality of the skin. We identified 660 pathogenic or likely pathogenic variants, including 241 novel variants, associated with over 342 known genetic conditions. The highly consanguineous nature of this cohort led to the diagnosis of autosomal recessive disorders in the majority of patients (79.1%) and allowed us to determine the shared carrier status of couples for suspected recessive phenotypes in their deceased child(ren) when direct testing was not possible. We also highlight the observations of recessive inheritance of genes previously associated only with dominant disorders and provide an expanded genotype-phenotype spectrum for multiple less-characterized genes. We present the largest mutational spectrum of known Mendelian disease, including possible founder variants, throughout the Iranian population, which can serve as a unique resource for clinical genomic studies locally and beyond.
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Affiliation(s)
- Ayda Abolhassani
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zohreh Fattahi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Mahsa Fadaee
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Raheleh Vazehan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Ahangari
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Shima Dehdahsi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Elham Parsimehr
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zahra Kalhor
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Peymani
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Noudehi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Fatehi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Fariba Afroozan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Hilda Yazdan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Bita Bozorgmehr
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Azita Azarkeivan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Nasle Salem Genetic Counseling Center, Bandar Abbas, Iran
| | - Farzad Fatehi
- Department of Neurology, Neuromuscular Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Payman Jamali
- Genetic Counseling Center, Shahroud Welfare Organization, Semnan, Iran
| | | | - Parvaneh Karimzadeh
- Pediatric Neurology Department, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Haleh Habibi
- Hamedan University of Medical Science, Hamedan, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahriar Nafissi
- Department of Neurology, Neuromuscular Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Hossein Najmabadi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran.
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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Alinaghi S, Mohseni M, Fattahi Z, Beheshtian M, Ghodratpour F, Zare Ashrafi F, Arzhangi S, Jalalvand K, Najafipour R, Khorram Khorshid HR, Kahrizi K, Najmabadi H. Genetic Analysis of 27 Y-STR Haplotypes in 11 Iranian Ethnic Groups. Arch Iran Med 2024; 27:79-88. [PMID: 38619031 PMCID: PMC11017261 DOI: 10.34172/aim.2024.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/23/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND The study of Y-chromosomal variations provides valuable insights into male susceptibility in certain diseases like cardiovascular disease (CVD). In this study, we analyzed paternal lineage in different Iranian ethnic groups, not only to identify developing medical etiology, but also to pave the way for gender-specific targeted strategies and personalized medicine in medical genetic research studies. METHODS The diversity of eleven Iranian ethnic groups was studied using 27 Y-chromosomal short tandem repeat (Y-STR) haplotypes from Y-filer® Plus kit. Analysis of molecular variance (AMOVA) based on pair-wise RST along with multidimensional scaling (MDS) calculation and Network phylogenic analysis was employed to quantify the differences between 503 unrelated individuals from each ethnicity. RESULTS Results from AMOVA calculation confirmed that Gilaks and Azeris showed the largest genetic distance (RST=0.35434); however, Sistanis and Lurs had the smallest considerable genetic distance (RST=0.00483) compared to other ethnicities. Although Azeris had a considerable distance from other ethnicities, they were still close to Turkmens. MDS analysis of ethnic groups gave the indication of lack of similarity between different ethnicities. Besides, network phylogenic analysis demonstrated insignificant clustering between samples. CONCLUSION The AMOVA analysis results explain that the close distance of Azeris and Turkmens may be the effect of male-dominant expansions across Central Asia that contributed to historical and demographics of populations in the region. Insignificant differences in network analysis could be the consequence of high mutation events that happened in the Y-STR regions over the years. Considering the ethnic group affiliations in medical research, our results provided an understanding and characterization of Iranian male population for future medical and population genetics studies.
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Affiliation(s)
- Somayeh Alinaghi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Ghodratpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Jalalvand
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Najafipour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Rashvand Z, Najmabadi H, Kahrizi K, Mozhdehipanah H, Moradi M, Estaki Z, Taherkhani K, Nikzat N, Najafipour R, Omrani MD. Identification of a Novel Variant in CC2D1A Gene Linked to Autosomal Recessive Intellectual Disability 3 in an Iranian Family and Investigating the Structure and Pleiotropic Effects of this Gene. Iran J Child Neurol 2024; 18:25-41. [PMID: 38375126 PMCID: PMC10874518 DOI: 10.22037/ijcn.v18i1.42188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 09/10/2023] [Indexed: 02/21/2024]
Abstract
Objectives Intellectual disability (ID) represents a significant health challenge due to its diverse and intricate nature. A multitude of genes play a role in brain development and function, with defects in these genes potentially leading to ID. Considering that many of these genes have yet to be identified, and those identified have only been found in a small number of patients, no complete description of the phenotype created by these genes is available. CC2D1A is one of the genes whose loss-of-function mutation leads to a rare form of non-syndromic ID-3(OMIM*610055), and four pathogenic variants have been reported in this gene so far. Materials & Methods n the current study, two affected females were included with an initial diagnosis of ID who were from an Iranian family with consanguineous marriage. Whole-exome sequencing was used to identify the probable genetic defects. The Genotypic and phenotypic characteristics of the patients were compared with a mutation in the CC2D1A gene, and then the structure of the gene and its reported variants were investigated. Results The patients carried a novel homozygous splicing variant (NM_017721, c.1641+1G>A) in intron 14, which is pathogenic according to the ACMG guideline. Loss-of-function mutations in CC2D1A have severe phenotypic consequences such as ID, autism spectrum disorder (ASD), and seizures. However, missense mutations lead to ASD with or without ID, and in some patients, they cause ciliopathy. Conclusion This study reports the fifth novel, probably pathogenic variant in the CC2D1A gene. Comparing the clinical and molecular genetic features of the patients with loss-of-function mutation helped to describe the phenotype caused by this gene more precisely. Investigating the CC2D1A gene's mutations and structure revealed that it performs multiple functions. The DM14 domain appears more pivotal in triggering severe clinical symptoms, including ID, than the C2 domain.
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Affiliation(s)
- Zahra Rashvand
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, the University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, the University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Mozhdehipanah
- Depatment of Neurology Boali Hospital, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mohammad Moradi
- Cellular and Molecular Research Centre, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Zohreh Estaki
- Department of Pediatric Dentistry, School of Dentistry, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Khadijeh Taherkhani
- Cellular and Molecular Research Centre, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Nooshin Nikzat
- Genetics Research Center, the University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Najafipour
- Genetics Research Center, the University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Mahmoudi-Aznaveh A, Tavoosidana G, Najmabadi H, Azizi Z, Ardestani A. The liver-derived exosomes stimulate insulin gene expression in pancreatic beta cells under condition of insulin resistance. Front Endocrinol (Lausanne) 2023; 14:1303930. [PMID: 38027137 PMCID: PMC10661932 DOI: 10.3389/fendo.2023.1303930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction An insufficient functional beta cell mass is a core pathological hallmark of type 2 diabetes (T2D). Despite the availability of several effective pharmaceuticals for diabetes management, there is an urgent need for novel medications to protect pancreatic beta cells under diabetic conditions. Integrative organ cross-communication controls the energy balance and glucose homeostasis. The liver and pancreatic islets have dynamic cross-communications where the liver can trigger a compensatory beta cell mass expansion and enhanced hormonal secretion in insulin-resistant conditions. However, the indispensable element(s) that foster beta cell proliferation and insulin secretion have yet to be completely identified. Exosomes are important extracellular vehicles (EVs) released by most cell types that transfer biological signal(s), including metabolic messengers such as miRNA and peptides, between cells and organs. Methods We investigated whether beta cells can take up liver-derived exosomes and examined their impact on beta cell functional genes and insulin expression. Exosomes isolated from human liver HepG2 cells were characterized using various methods, including Transmission Electron Microscopy (TEM), dynamic light scattering (DLS), and Western blot analysis of exosomal markers. Exosome labeling and cell uptake were assessed using CM-Dil dye. The effect of liver cell-derived exosomes on Min6 beta cells was determined through gene expression analyses of beta cell markers and insulin using qPCR, as well as Akt signaling using Western blotting. Results Treatment of Min6 beta cells with exosomes isolated from human liver HepG2 cells treated with insulin receptor antagonist S961 significantly increased the expression of beta cell markers Pdx1, NeuroD1, and Ins1 compared to the exosomes isolated from untreated cells. In line with this, the activity of AKT kinase, an integral component of the insulin receptor pathway, is elevated in pancreatic beta cells, as represented by an increase in AKT's downstream substrate, FoxO1 phosphorylation. Discussions This study suggests that liver-derived exosomes may carry a specific molecular cargo that can affect insulin expression in pancreatic beta cells, ultimately affecting glucose homeostasis.
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Affiliation(s)
- Azam Mahmoudi-Aznaveh
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholamreza Tavoosidana
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zahra Azizi
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Amin Ardestani
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Centre for Biomolecular Interactions Bremen, University of Bremen, Bremen, Germany
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7
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Bazazzadegan N, Abedini SS, Azarkeivan A, Banihashemi S, Nikzat N, Najmabadi H, Neishabury M. The Spectrum of HBB Mutations among 2315 Beta Thalassemia Patients of a Reference Clinic in Tehran-Iran. Hemoglobin 2023; 47:147-151. [PMID: 37548174 DOI: 10.1080/03630269.2023.2242787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 07/21/2023] [Indexed: 08/08/2023]
Abstract
Beta Thalassemia is the most prevalent and well-studied single gene disorder in Iran. Here, we investigated the spectrum of HBB gene mutations, identified among 2315 patients, referred to a reference thalassemia clinic in Tehran, on the basis of suspicion to thalassemia major or intermedia. The patients were homozygous or compound heterozygous for HBB mutations, and were referred from various Iranian provinces, during 15 years (2001- 2016). The HBB mutations were classified based on their frequency, and the result was compared to a meta-analysis of 14,293 beta thalassemia cases in the Iranian population, within the same time period. The mutation spectrum in this study contained 43 HBB mutations, compared to the 90, presented by the meta-analysis. Similar to the meta-analysis, IVSII-1 (G > A) and IVSI-5 (G > C) were the most common mutations in this study. These two comprised 62.40% of the total HBB mutant alleles in the studied population, comparable to 51.92% of that in the meta-analysis. IVSII-1 (G > A) and IVSI-5 (G > C), followed by 17 other mutations that had frequencies ranging from 0.15% to 5.44%, were among the 20 common HBB mutations in Iran and neighboring countries, according to the meta-analysis. This study provided further evidence to support the spectrum of the most common HBB mutations in the Iranian population.
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Affiliation(s)
- Niloofar Bazazzadegan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Seyedeh Sedigheh Abedini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Azita Azarkeivan
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
- Iranian Blood Transfusion Organization, Thalassemia Clinic, Tehran, Iran
| | - Susan Banihashemi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Nooshin Nikzat
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Neishabury
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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8
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Pagnamenta AT, Belles RS, Salbert BA, Wentzensen IM, Guillen Sacoto MJ, Santos FJR, Caffo A, Ferla M, Banos‐Pinero B, Pawliczak K, Makvand M, Najmabadi H, Maroofian R, Lester T, Yanez‐Felix AL, Villarroel‐Cortes CE, Xia F, Al Fayez K, Al Hashem A, Shears D, Irving M, Offiah AC, Kariminejad A, Taylor JC. The prevalence and phenotypic range associated with biallelic PKDCC variants. Clin Genet 2023; 104:121-126. [PMID: 36896672 PMCID: PMC10952701 DOI: 10.1111/cge.14324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/08/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023]
Abstract
PKDCC encodes a component of Hedgehog signalling required for normal chondrogenesis and skeletal development. Although biallelic PKDCC variants have been implicated in rhizomelic shortening of limbs with variable dysmorphic features, this association was based on just two patients. In this study, data from the 100 000 Genomes Project was used in conjunction with exome sequencing and panel-testing results accessed via international collaboration to assemble a cohort of eight individuals from seven independent families with biallelic PKDCC variants. The allelic series included six frameshifts, a previously described splice-donor site variant and a likely pathogenic missense variant observed in two families that was supported by in silico structural modelling. Database queries suggested that the prevalence of this condition is between 1 of 127 and 1 of 721 in clinical cohorts with skeletal dysplasia of unknown aetiology. Clinical assessments, combined with data from previously published cases, indicate a predominantly upper limb involvement. Micrognathia, hypertelorism and hearing loss appear to be commonly co-occurring features. In conclusion, this study strengthens the link between biallelic inactivation of PKDCC and rhizomelic limb-shortening and will enable clinical testing laboratories to better interpret variants in this gene.
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Affiliation(s)
- Alistair T. Pagnamenta
- NIHR Biomedical Research Centre, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | | | | | | | | | - Francis Jeshira Reynoso Santos
- Joe DiMaggio Children's HospitalHollywoodFloridaUSA
- Division of Human GeneticsChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvaniaUSA
| | - Alesky Caffo
- Joe DiMaggio Children's HospitalHollywoodFloridaUSA
| | - Matteo Ferla
- NIHR Biomedical Research Centre, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Benito Banos‐Pinero
- Oxford Genetics LaboratoriesOxford University Hospitals NHS Foundation Trust, The Churchill HospitalOxfordUK
| | | | - Mina Makvand
- Kariminejad‐Najmabadi Pathology & Genetics CenterTehranIran
| | - Hossein Najmabadi
- Kariminejad‐Najmabadi Pathology & Genetics CenterTehranIran
- Genetics Research CenterUniversity of Social Welfare & Rehabilitation ScienceTehranIran
| | | | - Reza Maroofian
- Department of Neuromuscular DiseasesUCL Queen Square Institute of Neurology, University College LondonLondonUK
| | - Tracy Lester
- Oxford Genetics LaboratoriesOxford University Hospitals NHS Foundation Trust, The Churchill HospitalOxfordUK
| | | | | | - Fan Xia
- Baylor GeneticsHoustonTexasUSA
| | - Khowla Al Fayez
- Department of Pediatrics, Division of Clinical Genetic and Metabolic MedicinePrince Sultan Medical Military CityRiyadhSaudi Arabia
| | - Amal Al Hashem
- Department of Pediatrics, Division of Clinical Genetic and Metabolic MedicinePrince Sultan Medical Military CityRiyadhSaudi Arabia
| | - Deborah Shears
- Oxford Centre for Genomic MedicineOxford University Hospitals NHS Foundation TrustOxfordUK
| | - Melita Irving
- Department of Clinical GeneticsGuy's and St Thomas' NHS Foundation TrustLondonUK
| | - Amaka C. Offiah
- Department of Oncology & MetabolismUniversity of SheffieldSheffieldUK
| | | | - Jenny C. Taylor
- NIHR Biomedical Research Centre, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
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9
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Goleyjani Moghadam M, Elahi Z, Soveyzi M, Arzhangi S, Nafissi S, Najmabadi H, Kahrizi K, Fattahi Z. Expanding the Molecular Spectrum of HK1-Related Charcot-Marie-Tooth Disease, Type 4G; the First Report in Iran. Arch Iran Med 2023; 26:279-284. [PMID: 38301092 PMCID: PMC10685863 DOI: 10.34172/aim.2023.43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/05/2023] [Indexed: 02/03/2024]
Abstract
Charcot-Marie-Tooth disease type 4G (CMT4G) was first reported in Balkan Gypsies as a myelinopathy starting with progressive distal lower limb weakness, followed by upper limb involvement and prominent distal sensory impairment later in the patient's life. So far, CMT4G has been only reported in European Roma communities with two founder homozygous variants; g.9712G>C and g.11027G>A, located in the 5'-UTR of the HK1 gene. Here, we present the first Iranian CMT4G patient manifesting progressive distal lower limb weakness from 11 years of age and diagnosed with chronic demyelinating sensorimotor polyneuropathy. Whole-exome sequencing for this patient revealed a homozygous c.19C>T (p. Arg7*) variant in the HK1 gene. This report expands the mutational spectrum of the HK1-related CMT disorder and provides supporting evidence for the observation of CMT4G outside the Roma population. Interestingly, the same Arg7* variant is recently observed in another unrelated Pakistani CMT patient, proposing a possible prevalence of this variant in the Middle Eastern populations.
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Affiliation(s)
| | - Zohreh Elahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Mohamad Soveyzi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahriar Nafissi
- Iranian Neuromuscular Research Center (INMRC), Tehran University of Medical Sciences, Tehran, Iran
- Department of Neurology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
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10
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Zare Ashrafi F, Akhtarkhavari T, Fattahi Z, Asadnezhad M, Beheshtian M, Arzhangi S, Najmabadi H, Kahrizi K. Emerging Epidemiological Data on Rare Intellectual Disability Syndromes from Analyzing the Data of a Large Iranian Cohort. Arch Iran Med 2023; 26:186-197. [PMID: 38301078 PMCID: PMC10685746 DOI: 10.34172/aim.2023.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 02/25/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND Intellectual disability (ID) is a genetically heterogeneous condition, and so far, 1679 human genes have been identified for this phenotype. Countries with a high rate of parental consanguinity, such as Iran, provide an excellent opportunity to identify the remaining novel ID genes, especially those with an autosomal recessive (AR) mode of inheritance. This study aimed to investigate the most prevalent ID genes identified via next-generation sequencing (NGS) in a large ID cohort at the Genetics Research Center (GRC) of the University of Social Welfare and Rehabilitation Sciences. METHODS First, we surveyed the epidemiological data of 619 of 1295 families in our ID cohort, who referred to the Genetics Research Center from all over the country between 2004 and 2021 for genetic investigation via the NGS pipeline. We then compared our data with those of several prominent studies conducted in consanguineous countries. Data analysis, including cohort data extraction, categorization, and comparison, was performed using the R program version 4.1.2. RESULTS We categorized the most common ID genes that were mutated in more than two families into 17 categories. The most common syndromic ID in our cohort was AP4 deficiency syndrome, and the most common non-syndromic autosomal recessive intellectual disability (ARID) gene was ASPM. We identified two unrelated families for the 36 ID genes. We found 14 genes in common between our cohort and the Arab and Pakistani groups, of which three genes (AP4M1, AP4S1, and ADGRG1) were repeated more than once. CONCLUSION To date, there has been no comprehensive targeted NGS platform for the detection of ID genes in our country. Due to the large sample size of our study, our data may provide the initial step toward designing an indigenously targeted NGS platform for the diagnosis of ID, especially common ARID in our population.
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Affiliation(s)
- Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Asadnezhad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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11
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Jamshidi F, Shokouhian E, Mohseni M, Kahrizi K, Najmabadi H, Babanejad M. Identification of a homozygous frameshift mutation in the FGF3 gene in a consanguineous Iranian family: First report of labyrinthine aplasia, microtia, and microdontia syndrome in Iran and literature review. Mol Genet Genomic Med 2023; 11:e2168. [PMID: 36934406 PMCID: PMC10178790 DOI: 10.1002/mgg3.2168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/20/2023] Open
Abstract
BACKGROUND To date, over 400 syndromes with hearing impairment have been identified which altogether constitute almost 30% of hereditary hearing loss (HL) cases around the globe. Manifested as complete or partial labyrinthine aplasia (severe malformations of the inner ear structure), type I microtia (smaller outer ear with shortened auricles), and microdontia (small and widely spaced teeth), labyrinthine aplasia, microtia, and microdontia (LAMM) syndrome (OMIM 610706) is an extremely rare autosomal recessive condition caused by bi-allelic mutations in the FGF3 gene. METHODS Using the whole-exome sequencing (WES) data of the proband, we analyzed a consanguineous Iranian family with three affected members presenting with congenital bilateral HL, type I microtia, and microdontia. RESULTS We discovered the homozygous deletion c.45delC in the first exon of the FGF3 gene, overlapping a 38.72 Mb homozygosity region in chromosome 11. Further investigations using Sanger sequencing revealed that this variant co-segregated with the phenotype observed in the family. CONCLUSION Here, we report the first identified case of LAMM syndrome in Iran, and by identifying a frameshift variant in the first exon of the FGF3 gene, our result will help better clarify the phenotype-genotype relation of LAMM syndrome.
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Affiliation(s)
- Fereshteh Jamshidi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Koodakyar Alley, Daneshjoo Blvd., Evin St., 1985713834, Tehran, Iran
| | - Ebrahim Shokouhian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Koodakyar Alley, Daneshjoo Blvd., Evin St., 1985713834, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Koodakyar Alley, Daneshjoo Blvd., Evin St., 1985713834, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Koodakyar Alley, Daneshjoo Blvd., Evin St., 1985713834, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Koodakyar Alley, Daneshjoo Blvd., Evin St., 1985713834, Tehran, Iran
| | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Koodakyar Alley, Daneshjoo Blvd., Evin St., 1985713834, Tehran, Iran
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12
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Mohseni M, Mohammadi Y, Zare Ashrafi F, Ghodratpour F, Jalalvand K, Arzhangi S, Babanejad M, Azizi MH, Kahrizi K, Najmabadi H. An Extended Iranian Family with Autosomal Dominant Non-syndromic Hearing Loss Associated with A Nonsense Mutation in the DIAPH1 Gene. Arch Iran Med 2023; 26:176-180. [PMID: 37543941 PMCID: PMC10685723 DOI: 10.34172/aim.2023.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/19/2023] [Indexed: 08/08/2023]
Abstract
Genetic analysis of non-syndromic hearing loss (NSHL) has been challenged due to marked clinical and genetic heterogeneity. Today, advanced next-generation sequencing (NGS) technologies, such as exome sequencing (ES), have drastically increased the efficacy of gene identification in heterogeneous Mendelian disorders. Here, we present the utility of ES and re-evaluate the phenotypic data for identifying candidate causal variants for previously unexplained progressive moderate to severe NSHL in an extended Iranian family. Using this method, we identified a known heterozygous nonsense variant in exon 26 of the DIAPH1 gene (MIM: 602121), which led to "Deafness, autosomal dominant 1, with or without thrombocytopenia; DFNA1" (MIM: 124900) in this large family in the absence of GJB2 disease-causing variants and also OtoSCOPE-negative results. To the best of our knowledge, this nonsense variant (NM_001079812.3):c.3610C>T (p.Arg1204Ter) is the first report of the DIAPH1 gene variant for autosomal dominant non-syndromic hearing loss (ADNSHL) in Iran.
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Affiliation(s)
- Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Yusuf Mohammadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Ghodratpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Jalalvand
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohammad Hossein Azizi
- Associate Professor of Otolaryngology, Academy of Medical Sciences of IR Iran, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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13
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Dawood M, Akay G, Mitani T, Marafi D, Fatih JM, Gezdirici A, Najmabadi H, Kahrizi K, Punetha J, Grochowski CM, Du H, Jolly A, Li H, Coban-Akdemir Z, Sedlazeck FJ, Hunter JV, Jhangiani SN, Muzny D, Pehlivan D, Posey JE, Carvalho CM, Gibbs RA, Lupski JR. A biallelic frameshift indel in PPP1R35 as a cause of primary microcephaly. Am J Med Genet A 2023; 191:794-804. [PMID: 36598158 PMCID: PMC9928800 DOI: 10.1002/ajmg.a.63080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/05/2022] [Accepted: 12/01/2022] [Indexed: 01/05/2023]
Abstract
Protein phosphatase 1 regulatory subunit 35 (PPP1R35) encodes a centrosomal protein required for recruiting microtubule-binding elongation machinery. Several proteins in this centriole biogenesis pathway correspond to established primary microcephaly (MCPH) genes, and multiple model organism studies hypothesize PPP1R35 as a candidate MCPH gene. Here, using exome sequencing (ES) and family-based rare variant analyses, we report a homozygous, frameshifting indel deleting the canonical stop codon in the last exon of PPP1R35 [Chr7: c.753_*3delGGAAGCGTAGACCinsCG (p.Trp251Cysfs*22)]; the variant allele maps in a 3.7 Mb block of absence of heterozygosity (AOH) in a proband with severe MCPH (-4.3 SD at birth, -6.1 SD by 42 months), pachygyria, and global developmental delay from a consanguineous Turkish kindred. Droplet digital PCR (ddPCR) confirmed mutant mRNA expression in fibroblasts. In silico prediction of the translation of mutant PPP1R35 is expected to be elongated by 18 amino acids before encountering a downstream stop codon. This complex indel allele is absent in public databases (ClinVar, gnomAD, ARIC, 1000 genomes) and our in-house database of 14,000+ exomes including 1800+ Turkish exomes supporting predicted pathogenicity. Comprehensive literature searches for PPP1R35 variants yielded two probands affected with severe microcephaly (-15 SD and -12 SD) with the same homozygous indel from a single, consanguineous, Iranian family from a cohort of 404 predominantly Iranian families. The lack of heterozygous cases in two large cohorts representative of the genetic background of these two families decreased our suspicion of a founder allele and supports the contention of a recurrent mutation. We propose two potential secondary structure mutagenesis models for the origin of this variant allele mediated by hairpin formation between complementary GC rich segments flanking the stop codon via secondary structure mutagenesis.
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Affiliation(s)
- Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul 34480, Turkey
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | | | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - He Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Fritz J. Sedlazeck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill V. Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, 77030, USA
- E.B. Singleton Department of Pediatric Radiology, Texas Children’s Hospital, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Shalini N. Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Claudia M.B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Pacific Northwest Research Institute, Seattle, WA, 98122, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030
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14
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Zare Ashrafi F, Mohseni M, Beheshtian M, Fattahi Z, Ghodratpour F, Keshavarzi F, Behravan H, Kalhor M, Jalalvand K, Azad M, Koshki M, Jafarpour A, Ghaziasadi A, Abdollahi A, Kiani SJ, Ataei-Pirkooh A, Rezaei Azhar I, Bokharaei-Salim F, Haghshenas MR, Babamahmoodi F, Mokhames Z, Soleimani A, Ziaee M, Javanmard D, Ghafari S, Ezani A, Ansari Moghaddam A, Shahraki-Sanavi F, Hashemi Shahri SM, Azaran A, Yousefi F, Moattari A, Moghadami M, Fakhim H, Ataei B, Nasri E, Poortahmasebi V, Varshochi M, Mojtahedi A, Jalilian F, Khazeni M, Moradi A, Tabarraei A, Piroozmand A, Yahyapour Y, Bayani M, Aboofazeli A, Ghafari P, Keramat F, Tavakoli M, Jalali T, Pouriayevali MH, Salehi-Vaziri M, Khorram Khorshid HR, Najafipour R, Malekzadeh R, Kahrizi K, Jazayeri SM, Najmabadi H. Implementation of an In-House Platform for Rapid Screening of SARS-CoV-2 Genome Variations. Arch Iran Med 2023; 26:69-75. [PMID: 37543926 PMCID: PMC10685895 DOI: 10.34172/aim.2023.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/16/2022] [Indexed: 08/08/2023]
Abstract
BACKGROUND Global real-time monitoring of SARS-CoV-2 variants is crucial to controlling the COVID-19 outbreak. The purpose of this study was to set up a Sanger-based platform for massive SARS-CoV-2 variant tracking in laboratories in low-resource settings. METHODS We used nested RT-PCR assay, Sanger sequencing and lineage assignment for 930-bp of the SARS-CoV-2 spike gene, which harbors specific variants of concern (VOCs) mutations. We set up our platform by comparing its results with whole genome sequencing (WGS) data on 137 SARS-CoV-2 positive samples. Then, we applied it on 1028 samples from March-September 2021. RESULTS In total, 125 out of 137 samples showed 91.24% concordance in mutation detection. In lineage assignment, 123 out of 137 samples demonstrated 89.78% concordance, 65 of which were assigned as VOCs and showed 100% concordance. Of 1028 samples screened by our in-house method, 78 distinct mutations were detected. The most common mutations were: S:D614G (21.91%), S:P681R (12.19%), S:L452R (12.15%), S:T478K (12.15%), S:N501Y (8.91%), S:A570D (8.89%), S:P681H (8.89%), S:T716I (8.74%), S:L699I (3.50%) and S:S477N (0.28%). Of 1028 samples, 980 were attributed as VOCs, which include the Delta (B.1.617.2) and Alpha (B.1.1.7) variants. CONCLUSION Our proposed in-house Sanger-based assay for SARS-CoV-2 lineage assignment is an accessible strategy in countries with poor infrastructure facilities. It can be applied in the rapid tracking of SARS-CoV-2 VOCs in the SARS-CoV-2 pandemic.
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Affiliation(s)
- Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Ghodratpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Keshavarzi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hanieh Behravan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Marzieh Kalhor
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Jalalvand
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Azad
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Mahdieh Koshki
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Ali Jafarpour
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
- Gerash Amir-al-Momenin Medical and Educational Center, Gerash University of Medical Sciences, Gerash, Iran
| | - Azam Ghaziasadi
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Abdollahi
- Department of Pathology, School of Medicine, Imam Khomeini Hospital, Tehran University of Medical Sciences, Iran
| | - Seyed Jalal Kiani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Angila Ataei-Pirkooh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Iman Rezaei Azhar
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Farah Bokharaei-Salim
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Haghshenas
- Department of Medical Microbiology, Antimicrobial Resistance Research Center, Communicable Diseases Institute, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Farhang Babamahmoodi
- Department of Medical Microbiology, Antimicrobial Resistance Research Center, Communicable Diseases Institute, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zakiye Mokhames
- Department of Molecular Diagnostic, Emam Ali Educational and Therapeutic Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Alireza Soleimani
- Department of Infectious Diseases, Imam Ali hospital, Alborz University of Medical Sciences, Karaj, Iran
| | - Masood Ziaee
- Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Davod Javanmard
- Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Shokouh Ghafari
- Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Akram Ezani
- Qazvin Deputy of Treatment Reference Laboratory, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | | | | | - Azarakhsh Azaran
- Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farid Yousefi
- Department of Infectious Diseases, School of Medicine, Razi Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Afagh Moattari
- Department of Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohsen Moghadami
- Health policy research center, Shiraz University of medical sciences, Shiraz, Iran
| | - Hamed Fakhim
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Behrooz Ataei
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elahe Nasri
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Vahdat Poortahmasebi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mojtaba Varshochi
- Infectious and Tropical Disease Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Ali Mojtahedi
- Microbiology Department, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Farid Jalilian
- Department of Medical Virology, Faculty of Medicine, Hamadan University of Medical sciences, Hamadan, Iran
| | | | | | | | - Ahmad Piroozmand
- Department of Microbiology, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Yousef Yahyapour
- Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran
| | - Masoumeh Bayani
- Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran
| | - Amir Aboofazeli
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Parsa Ghafari
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Fariba Keramat
- Brucellosis Research Center, Hamedan University of Medical Science, Hamadan, Iran
| | - Mahsa Tavakoli
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran
| | - Tahmineh Jalali
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran
- Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Hassan Pouriayevali
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran
- Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran
| | - Mostafa Salehi-Vaziri
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran
- Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran
| | | | - Reza Najafipour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Cell and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Reza Malekzadeh
- Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
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15
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Elahi Z, Soveyzi M, Nafissi S, Nilipour Y, Goleyjani Moghadam M, Keshavarz E, Kariminejad A, Najmabadi H, Fattahi Z. Bi-allelic loss of function variant in the NRCAM gene is associated with motor-predominant axonal polyneuropathy; the second report. Mol Genet Genomic Med 2023; 11:e2131. [PMID: 36606341 PMCID: PMC10094081 DOI: 10.1002/mgg3.2131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The role of biallelic variants in the NRCAM gene underlying a neurodevelopmental disorder has been defined recently. The phenotype is mainly recognized by varying severity of global developmental delay/intellectual disability, hypotonia, spasticity, and peripheral neuropathy. METHODS Here, we describe a patient with an initial diagnosis of motor-predominant axonal polyneuropathy or a form of distal SMA. Whole-exome sequencing (WES), in parallel with WES-based CNV detection and assessment of homozygosity runs, was performed to identify this patient's possible genetic cause. RESULTS Whole exome sequencing revealed a homozygous variant, c.73C > T (p.Gln25*), in the NRCAM gene, while the patient manifests a mild range of phenotypes compared to NRCAM-related disorder. He presented only motor-predominant axonal polyneuropathy with no other signs of central nervous system involvement. CONCLUSIONS This study is the second report of an association between biallelic NRCAM gene variants and a Mendelian disorder. The obtained clinical data, together with the molecular findings in this patient, expands the clinical and molecular spectrum of NRCAM-related disorder and highlights its phenotypic complexity. Although patients with loss of function variants in this gene have previously presented severe clinical features, we show that type of the pathogenic variant does not necessarily determine the severity of this phenotype.
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Affiliation(s)
- Zohreh Elahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Mohamad Soveyzi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahriar Nafissi
- Neuromuscular Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Neurology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Yalda Nilipour
- Pediatric Pathology Research Center, Research Institute for Children's Health, Mofid Children Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Elham Keshavarz
- Department of Radiology, Mahdiyeh Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
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16
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Mensah MA, Niskanen H, Magalhaes AP, Basu S, Kircher M, Sczakiel HL, Reiter AMV, Elsner J, Meinecke P, Biskup S, Chung BHY, Dombrowsky G, Eckmann-Scholz C, Hitz MP, Hoischen A, Holterhus PM, Hülsemann W, Kahrizi K, Kalscheuer VM, Kan A, Krumbiegel M, Kurth I, Leubner J, Longardt AC, Moritz JD, Najmabadi H, Skipalova K, Snijders Blok L, Tzschach A, Wiedersberg E, Zenker M, Garcia-Cabau C, Buschow R, Salvatella X, Kraushar ML, Mundlos S, Caliebe A, Spielmann M, Horn D, Hnisz D. Aberrant phase separation and nucleolar dysfunction in rare genetic diseases. Nature 2023; 614:564-571. [PMID: 36755093 PMCID: PMC9931588 DOI: 10.1038/s41586-022-05682-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/22/2022] [Indexed: 02/10/2023]
Abstract
Thousands of genetic variants in protein-coding genes have been linked to disease. However, the functional impact of most variants is unknown as they occur within intrinsically disordered protein regions that have poorly defined functions1-3. Intrinsically disordered regions can mediate phase separation and the formation of biomolecular condensates, such as the nucleolus4,5. This suggests that mutations in disordered proteins may alter condensate properties and function6-8. Here we show that a subset of disease-associated variants in disordered regions alter phase separation, cause mispartitioning into the nucleolus and disrupt nucleolar function. We discover de novo frameshift variants in HMGB1 that cause brachyphalangy, polydactyly and tibial aplasia syndrome, a rare complex malformation syndrome. The frameshifts replace the intrinsically disordered acidic tail of HMGB1 with an arginine-rich basic tail. The mutant tail alters HMGB1 phase separation, enhances its partitioning into the nucleolus and causes nucleolar dysfunction. We built a catalogue of more than 200,000 variants in disordered carboxy-terminal tails and identified more than 600 frameshifts that create arginine-rich basic tails in transcription factors and other proteins. For 12 out of the 13 disease-associated variants tested, the mutation enhanced partitioning into the nucleolus, and several variants altered rRNA biogenesis. These data identify the cause of a rare complex syndrome and suggest that a large number of genetic variants may dysregulate nucleoli and other biomolecular condensates in humans.
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Affiliation(s)
- Martin A. Mensah
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Henri Niskanen
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexandre P. Magalhaes
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Shaon Basu
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Kircher
- grid.484013.a0000 0004 6879 971XExploratory Diagnostic Sciences, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.4562.50000 0001 0057 2672Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel Germany
| | - Henrike L. Sczakiel
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alisa M. V. Reiter
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jonas Elsner
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Meinecke
- grid.13648.380000 0001 2180 3484Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Saskia Biskup
- grid.498061.20000 0004 6008 5552Center for Genomics and Transcriptomics (CeGaT), Tübingen, Germany
| | - Brian H. Y. Chung
- grid.194645.b0000000121742757Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Gregor Dombrowsky
- grid.412468.d0000 0004 0646 2097Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany ,grid.5560.60000 0001 1009 3608Department of Medical Genetics, Carl von Ossietzky University, Oldenburg, Germany
| | - Christel Eckmann-Scholz
- grid.412468.d0000 0004 0646 2097Department of Obstetrics and Gynecology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Marc Phillip Hitz
- grid.412468.d0000 0004 0646 2097Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital Schleswig-Holstein, Kiel, Germany ,grid.5560.60000 0001 1009 3608Department of Medical Genetics, Carl von Ossietzky University, Oldenburg, Germany
| | - Alexander Hoischen
- grid.10417.330000 0004 0444 9382Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul-Martin Holterhus
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, Pediatric Endocrinology and Diabetes, University Hospital Schleswig-Holstein, Schleswig-Holstein, Germany
| | - Wiebke Hülsemann
- grid.440182.b0000 0004 0580 3398Handchirurgie, Katholisches Kinderkrankenhaus Wilhelmstift, Hamburg, Germany
| | - Kimia Kahrizi
- grid.472458.80000 0004 0612 774XGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Vera M. Kalscheuer
- grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Anita Kan
- grid.415550.00000 0004 1764 4144Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Mandy Krumbiegel
- grid.5330.50000 0001 2107 3311Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Ingo Kurth
- grid.412301.50000 0000 8653 1507Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University Hospital, Aachen, Germany
| | - Jonas Leubner
- grid.6363.00000 0001 2218 4662Department of Pediatric Neurology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ann Carolin Longardt
- grid.412468.d0000 0004 0646 2097Department of Pediatrics, University Hospital Center Schleswig‐Holstein, Kiel, Germany
| | - Jörg D. Moritz
- grid.412468.d0000 0004 0646 2097Department of Radiology and Neuroradiology, Pediatric Radiology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Hossein Najmabadi
- grid.472458.80000 0004 0612 774XGenetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Karolina Skipalova
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lot Snijders Blok
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andreas Tzschach
- grid.5963.9Institute of Human Genetics, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eberhard Wiedersberg
- grid.491868.a0000 0000 9601 2399Zentrum für Kinder-und Jugendmedizin, Helios Kliniken Schwerin, Schwerin, Germany
| | - Martin Zenker
- grid.5807.a0000 0001 1018 4307Institute of Human Genetics, University Hospital, Otto-von-Guericke University, Magdeburg, Germany
| | - Carla Garcia-Cabau
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - René Buschow
- grid.419538.20000 0000 9071 0620Microscopy Core Facility, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Xavier Salvatella
- grid.473715.30000 0004 6475 7299Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain ,grid.425902.80000 0000 9601 989XICREA, Passeig Lluís Companys 23, Barcelona, Spain
| | - Matthew L. Kraushar
- grid.419538.20000 0000 9071 0620Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Stefan Mundlos
- grid.6363.00000 0001 2218 4662Institute of Medical Genetics and Human Genetics, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany ,grid.484013.a0000 0004 6879 971XBIH Biomedical Innovation Academy, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany ,grid.419538.20000 0000 9071 0620RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany ,grid.506128.8BCRT-Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Almuth Caliebe
- grid.4562.50000 0001 0057 2672Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel Germany
| | - Malte Spielmann
- RG Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany. .,Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany. .,DZHK (German Centre for Cardiovascular Research), partner site Hamburg, Lübeck, Kiel, Lübeck, Germany.
| | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Denes Hnisz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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17
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Ehtesham N, Mosallaei M, Beheshtian M, Khoshbakht S, Fadaee M, Vazehan R, Faraji Zonooz M, Karimzadeh P, Kahrizi K, Najmabadi H. Characterizing Genotypes and Phenotypes Associated with Dysfunction of Channel-Encoding Genes in a Cohort of Patients with Intellectual Disability. Arch Iran Med 2022; 25:788-797. [PMID: 37543906 PMCID: PMC10685845 DOI: 10.34172/aim.2022.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/20/2021] [Indexed: 08/08/2023]
Abstract
BACKGROUND Ion channel dysfunction in the brain can lead to impairment of neuronal membranes and generate several neurological diseases, especially neurodevelopmental disorders. METHODS In this study, we set out to delineate the genotype and phenotype spectrums of 14 Iranian patients from 7 families with intellectual disability (ID) and/or developmental delay (DD) in whom genetic mutations were identified by next-generation sequencing (NGS) in 7 channel-encoding genes: KCNJ10, KCNQ3, KCNK6, CACNA1C, CACNA1G, SCN8A, and GRIN2B. Moreover, the data of 340 previously fully reported ID and/or DD cases with a mutation in any of these seven genes were combined with our patients to clarify the genotype and phenotype spectrum in this group. RESULTS In total, the most common phenotypes in 354 cases with ID/DD in whom mutation in any of these 7 channel-encoding genes was identified were as follows: ID (77.4%), seizure (69.8%), DD (59.8%), behavioral abnormality (29.9%), hypotonia (21.7%), speech disorder (21.5%), gait disturbance (20.9%), and ataxia (20.3%). Electroencephalography abnormality (33.9%) was the major brain imaging abnormality. CONCLUSION The results of this study broaden the molecular spectrum of channel pathogenic variants associated with different clinical presentations in individuals with ID and/or DD.
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Affiliation(s)
- Naeim Ehtesham
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Meysam Mosallaei
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahrouz Khoshbakht
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mahsa Fadaee
- Kariminejad – Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Raheleh Vazehan
- Kariminejad – Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Parvaneh Karimzadeh
- Department of Pediatric Neurology, School of Medicine, Pediatric Neurology Research Center, Mofid Children’s Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad – Najmabadi Pathology & Genetics Center, Tehran, Iran
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18
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Mehrabi Sisakht J, Mehri M, Najmabadi H, Azarkeivan A, Neishabury M. Genetic Diagnosis of Pyruvate Kinase Deficiency in Undiagnosed Iranian Patients with Severe Hemolytic Anemia, using Whole Exome Sequencing. Arch Iran Med 2022; 25:691-697. [PMID: 37542401 PMCID: PMC10685872 DOI: 10.34172/aim.2022.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/28/2021] [Indexed: 08/06/2023]
Abstract
BACKGROUND After ruling out the most common causes of severe hemolytic anemia by routine diagnostic tests, certain patients remain without a diagnosis. The aim of this study was to elucidate the genetic cause of the disease in these patients using next generation sequencing (NGS). METHODS Four unrelated Iranian families including six blood transfusion dependent cases and their parents were referred to us from a specialist center in Tehran. There was no previous history of anemia in the families and the parents had no abnormal hematological presentations. All probands presented severe congenital hemolytic anemia, neonatal jaundice and splenomegaly. Common causes of hemolytic anemia were ruled out prior to this investigation in these patients and they had no diagnosis. Whole exome sequencing (WES) was performed in the probands and the results were confirmed by Sanger sequencing and subsequent family studies. RESULTS We identified five variants in the PKLR gene, including a novel unpublished frameshift in these families. These variants were predicted as pathogenic according to the ACMG guidelines by Intervar and/or Varsome prediction tools. Subsequent family studies by Sanger sequencing supported the diagnosis of pyruvate kinase deficiency (PKD) in six affected individuals and the carrier status of disease in their parents. CONCLUSION These findings show that PKD is among the rare blood disorders that could remain undiagnosed or even ruled out in Iranian population without performing NGS. This could be due to pitfalls in clinical, hematological or biochemical approaches in diagnosing PKD. Furthermore, genotyping PKD patients in Iran could reveal novel mutations in the PKLR gene.
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Affiliation(s)
- Jafar Mehrabi Sisakht
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maghsood Mehri
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology & Genetics Centre, Tehran, Iran
| | - Azita Azarkeivan
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Maryam Neishabury
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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19
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Hosseinpour M, Ardalani F, Mohseni M, Beheshtian M, Arzhangi S, Ossareh S, Najmabadi H, Nobakht A, Kahrizi K, Broumand B. Targeted Next Generation Sequencing Revealed Novel Variants in the PKD1 and PKD2 Genes of Iranian Patients with Autosomal Dominant Polycystic Kidney Disease. Arch Iran Med 2022; 25:600-608. [PMID: 37543885 PMCID: PMC10685772 DOI: 10.34172/aim.2022.95] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/10/2022] [Indexed: 08/07/2023]
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD), one of the common inherited disorders in humans, is characterized by the development and enlargement of renal cysts, often leading to end-stage renal disease (ESRD). In this study, Iranian ADPKD families were subjected to high-throughput DNA sequencing to find potential causative variants facilitating the way toward risk assessment and targeted therapy. METHODS Our protocol was based on the targeted next generation sequencing (NGS) panel previously developed in our center comprising 12 genes involved in PKD. This panel has been applied to investigate the genetic causes of 32 patients with a clinical suspicion of ADPKD. RESULTS We identified a total of 31 variants for 32 individuals, two of which were each detected in two individuals. Twenty-seven out of 31 detected variants were interpreted as pathogenic/likely pathogenic and the remaining 4 of uncertain significance with a molecular diagnostic success rate of 87.5%. Among these variants, 25 PKD1/2 pathogenic/likely pathogenic variants were detected in 32 index patients (78.1%), and variants of uncertain significance in four individuals (12.5% in PKD1/2). The majority of variants was identified in PKD1 (74.2%). Autosomal recessive PKD was identified in one patient, indicating the similarities between recessive and dominant PKD. In concordance with earlier studies, this biallelic PKD1 variant, p.Arg3277Cys, leads to rapidly progressive and severe disease with very early-onset ADPKD. CONCLUSION Our findings suggest that targeted gene panel sequencing is expected to be the method of choice to improve diagnostic and prognostic accuracy in PKD patients with heterogeneity in genetic background.
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Affiliation(s)
- Maryam Hosseinpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fariba Ardalani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahrzad Ossareh
- Division of Nephrology, Department of Medicine, Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Ali Nobakht
- Department of Nephrology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Behrooz Broumand
- Pars Advanced and Minimally Invasive Medical Manners Research Center, Pars Hospital, Tehran, Iran
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20
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Fattahi Z, Mohseni M, Beheshtian M, Jafarpour A, Jalalvand K, Keshavarzi F, Behravan H, Ghodratpour F, Zare Ashrafi F, Kalhor M, Azad M, Koshki M, Ghaziasadi A, Soveyzi M, Abdollahi A, Kiani SJ, Ataei-Pirkooh A, Rezaeiazhar I, Bokharaei-Salim F, Haghshenas MR, Babamahmoodi F, Mokhames Z, Soleimani A, Elahi Z, Ziaee M, Javanmard D, Ghafari S, Ezani A, Ansari Moghaddam A, Shahraki-Sanavi F, Hashemi Shahri SM, Azaran A, Yousefi F, Moattari A, Moghadami M, Fakhim H, Ataei B, Nasri E, Poortahmasebi V, Varshochi M, Mojtahedi A, Jalilian F, Khazeni M, Moradi A, Tabarraei A, Piroozmand A, Yahyapour Y, Bayani M, Tavangar F, Yaghoubi M, Keramat F, Tavakoli M, Jalali T, Pouriayevali MH, Salehi-Vaziri M, Khorram Khorshid HR, Najafipour R, Malekzadeh R, Kahrizi K, Jazayeri SM, Najmabadi H. Disease Waves of SARS-CoV-2 in Iran Closely Mirror Global Pandemic Trends. Arch Iran Med 2022; 25:508-522. [PMID: 37543873 DOI: 10.34172/aim.2022.83] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/17/2022] [Indexed: 08/07/2023]
Abstract
BACKGROUND Complete SARS-CoV-2 genome sequencing in the early phase of the outbreak in Iran showed two independent viral entries. Subsequently, as part of a genome surveillance project, we aimed to characterize the genetic diversity of SARS-CoV-2 in Iran over one year after emerging. METHODS We provided 319 SARS-CoV-2 whole-genome sequences used to monitor circulating lineages in March 2020-May 2021 time interval. RESULTS The temporal dynamics of major SARS-CoV-2 clades/lineages circulating in Iran is comparable to the global perspective and represent the 19A clade (B.4) dominating the first disease wave, followed by 20A (B.1.36), 20B (B.1.1.413), 20I (B.1.1.7), leading the second, third and fourth waves, respectively. We observed a mixture of circulating B.1.36, B.1.1.413, B.1.1.7 lineages in winter 2021, paralleled in a fading manner for B.1.36/B.1.1.413 and a growing rise for B.1.1.7, prompting the fourth outbreak. Entry of the Delta variant, leading to the fifth disease wave in summer 2021, was detected in April 2021. This study highlights three lineages as hallmarks of the SARS-CoV-2 outbreak in Iran; B4, dominating early periods of the epidemic, B.1.1.413 (B.1.1 with the combination of [D138Y-S477N-D614G] spike mutations) as a characterizing lineage in Iran, and the co-occurrence of [I100T-L699I] spike mutations in half of B.1.1.7 sequences mediating the fourth peak. It also designates the renowned combination of G and GR clades' mutations as the top recurrent mutations. CONCLUSION In brief, we provided a real-time and comprehensive picture of the SARS-CoV-2 genetic diversity in Iran and shed light on the SARS-CoV-2 transmission and circulation on the regional scale.
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Affiliation(s)
- Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Ali Jafarpour
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
- Gerash Amir-al-Momenin Medical and Educational Center, Gerash University of Medical Sciences, Gerash, Iran
| | - Khadijeh Jalalvand
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Keshavarzi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hanieh Behravan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Ghodratpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Marzieh Kalhor
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Azad
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Mahdieh Koshki
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Azam Ghaziasadi
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohamad Soveyzi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Alireza Abdollahi
- Department of Pathology, School of Medicine, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Jalal Kiani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Angila Ataei-Pirkooh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Iman Rezaeiazhar
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Farah Bokharaei-Salim
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Haghshenas
- Department of Medical Microbiology, Antimicrobial Resistance Research Center, Communicable Diseases Institute, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Farhang Babamahmoodi
- Department of Medical Microbiology, Antimicrobial Resistance Research Center, Communicable Diseases Institute, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zakiye Mokhames
- Department of Molecular Diagnostic, Emam Ali Educational and Therapeutic Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Alireza Soleimani
- Department of Infectious Diseases, Imam Ali hospital, Alborz University of Medical Sciences, Karaj, Iran
| | - Zohreh Elahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Masood Ziaee
- Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Davod Javanmard
- Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Shokouh Ghafari
- Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Akram Ezani
- Qazvin Deputy of Treatment Reference Laboratory, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | | | | | - Azarakhsh Azaran
- Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farid Yousefi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Afagh Moattari
- Department of Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohsen Moghadami
- Health Policy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamed Fakhim
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Behrooz Ataei
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elahe Nasri
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Vahdat Poortahmasebi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mojtaba Varshochi
- Infectious and Tropical Disease Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Ali Mojtahedi
- Microbiology Department, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Farid Jalilian
- Department of Medical Virology, Faculty of Medicine, Hamadan University of Medical sciences, Hamadan, Iran
| | | | | | | | - Ahmad Piroozmand
- Department of Microbiology, School Of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Yousef Yahyapour
- Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran
| | - Masoumeh Bayani
- Infectious Diseases and Tropical Medicine Research Center, Babol University of Medical Sciences, Babol, Iran
| | - Fatemeh Tavangar
- Iranian Blood Transfusion Research Center, High Institute for Education and Research in Transfusion Medicine, Tehran, Iran
| | | | - Fariba Keramat
- Brucellosis Research Center, Hamedan University of Medical Science, Hamadan, Iran
| | - Mahsa Tavakoli
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran
| | - Tahmineh Jalali
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran
- Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Hassan Pouriayevali
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran
- Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran
| | - Mostafa Salehi-Vaziri
- COVID-19 National Reference Laboratory, Pasteur Institute of Iran, Tehran, Iran
- Department of Arboviruses and Viral Hemorrhagic Fevers (National Reference Laboratory), Pasteur Institute of Iran, Tehran, Iran
| | | | - Reza Najafipour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Malekzadeh
- Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
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21
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Saghi M, InanlooRahatloo K, Alavi A, Kahrizi K, Najmabadi H. Intellectual disability associated with craniofacial dysmorphism due to POLR3B mutation and defect in spliceosomal machinery. BMC Med Genomics 2022; 15:89. [PMID: 35436926 PMCID: PMC9014605 DOI: 10.1186/s12920-022-01237-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 04/12/2022] [Indexed: 11/10/2022] Open
Abstract
Background Intellectual disability (ID) is a clinically important disease and a most prevalent neurodevelopmental disorder. The etiology and pathogenesis of ID are poorly recognized. Exome sequencing revealed a homozygous missense mutation in the POLR3B gene in a consanguineous family with three Intellectual disability with craniofacial anomalies patients. POLR3B gene encoding the second largest subunit of RNA polymerase III. Methods We performed RNA sequencing on blood samples to obtain insights into the biological pathways influenced by POLR3B mutation. We applied the results of our RNA-Seq analysis to several gene ontology programs such as ToppGene, Enrichr, KEGG. Results A significant decrease in expression of several spliceosomal RNAs, ribosomal proteins, and transcription factors was detected in the affected, compared to unaffected, family members. Conclusions We hypothesize that POLR3B mutation dysregulates the expression of some important transcription factors, ribosomal and spliceosomal genes, and impairments in protein synthesis and splicing mediated in part by transcription factors such as FOXC2 and GATA1 contribute to impaired neuronal function and concurrence of intellectual disability and craniofacial anomalies in our patients. Our study highlights the emerging role of the spliceosome and ribosomal proteins in intellectual disability. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01237-5.
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Affiliation(s)
- Mostafa Saghi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Afagh Alavi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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22
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Sotoudeh Anvari M, Vasei H, Najmabadi H, Badv RS, Golipour A, Mohammadi-Yeganeh S, Salehi S, Mohamadi M, Goodarzynejad H, Mowla SJ. Identification of microRNAs associated with human fragile X syndrome using next-generation sequencing. Sci Rep 2022; 12:5011. [PMID: 35322102 PMCID: PMC8943156 DOI: 10.1038/s41598-022-08916-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 03/15/2022] [Indexed: 11/09/2022] Open
Abstract
Fragile X syndrome (FXS) is caused by a mutation in the FMR1 gene which can lead to a loss or shortage of the FMR1 protein. This protein interacts with specific miRNAs and can cause a range of neurological disorders. Therefore, miRNAs could act as a novel class of biomarkers for common CNS diseases. This study aimed to test this theory by exploring the expression profiles of various miRNAs in Iranian using deep sequencing-based technologies and validating the miRNAs affecting the expression of the FMR1 gene. Blood samples were taken from 15 patients with FXS (9 males, 6 females) and 12 controls. 25 miRNAs were differentially expressed in individuals with FXS compared to controls. Levels of 9 miRNAs were found to be significantly changed (3 upregulated and 6 downregulated). In Patients, the levels of hsa-miR-532-5p, hsa-miR-652-3p and hsa-miR-4797-3p were significantly upregulated while levels of hsa-miR-191-5p, hsa-miR-181-5p, hsa-miR-26a-5p, hsa-miR-30e-5p, hsa-miR-186-5p, and hsa-miR-4797-5p exhibited significant downregulation; and these dysregulations were confirmed by RT-qPCR. This study presents among the first evidence of altered miRNA expression in blood samples from patients with FXS, which could be used for diagnostic, prognostic, and treatment purposes. Larger studies are required to confirm these preliminary results.
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Affiliation(s)
- Maryam Sotoudeh Anvari
- Department of Molecular Pathology, School of Medicine, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran.
| | - Hamed Vasei
- Department of Mathematical Science, Sharif University of Technology, Tehran, Iran
| | - Hossein Najmabadi
- Department of Genetics, School of Rehabilitation Sciences, Genetic Research Center, The University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Shervin Badv
- Department of Pediatrics, School of Medicine, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Akram Golipour
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Samira Mohammadi-Yeganeh
- Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeede Salehi
- Cell-Based Therapies Research Center, Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmood Mohamadi
- Department of Pediatrics, School of Medicine, Children's Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamidreza Goodarzynejad
- Department of Basic and Clinical Research, Tehran Heart Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.
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23
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Mosallaei M, Ehtesham N, Beheshtian M, Khoshbakht S, Davarnia B, Kahrizi K, Najmabadi H. Phenotype and genotype spectrum of variants in guanine nucleotide exchange factor genes in a broad cohort of Iranian patients. Mol Genet Genomic Med 2022; 10:e1894. [PMID: 35174982 PMCID: PMC9000939 DOI: 10.1002/mgg3.1894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 11/21/2022] Open
Abstract
Background Guanine nucleotide exchange factors (GEFs) play pivotal roles in neuronal cell functions by exchanging GDP to GTP nucleotide and activation of GTPases. We aimed to determine the genotype and phenotype spectrum of GEF mutations by collecting data from a large Iranian cohort with intellectual disability (ID) and/or developmental delay (DD). Methods We collected data from nine families with 20 patients extracted from Iranian cohort of 640 families with ID and/or DD. Next‐generation sequencing (NGS) was used to identify the causing variants in recruited families. We also compared our clinical and molecular findings with previously reported patients carrying mutations in these GEF genes in the literature published until mid‐2021. Results We identified disease‐causing variants in eight GEF genes including ALS2, IQSEC2, MADD, RAB3GAP1, RAB3GAP2, TRIO, ITSN1, and DENND2A. The major clinical manifestations in 203 previously reported cases along with our 20 patients with disease causing variants in eight GEF genes were as follow; speech disorder (85.2%), ID (81.6%), DD (81.1%), inability to walk (71.3%), facial dysmorphisms features (52.4%), abnormalities in skull morphology (55.6%), hypotonia and muscle weakness (47%), and brain MRI abnormalities (43.4%). Conclusion Our study provides new insights into the genotype and phenotype spectrum of mutations in GEF genes.
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Affiliation(s)
- Meysam Mosallaei
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Naeim Ehtesham
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahrouz Khoshbakht
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Behzad Davarnia
- Department of Genetic and Pathology, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology & Genetics Centre, Tehran, Iran
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24
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Sadighi G, Nazeri Astaneh A, Najmabadi H, Khodaei Ardakani MR, Latifi-Navid S. DNA Banking to Assess Genetic Influences on Schizophrenia. Med J Islam Repub Iran 2022; 36:42. [PMID: 36128322 PMCID: PMC9448483 DOI: 10.47176/mjiri.36.42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 04/27/2022] [Indexed: 11/09/2022] Open
Abstract
Background: Schizophrenia is among the most prevalent psychiatric disorders globally, with a lifetime prevalence rate of 0.3% to 0.7%, characterized by the heterogeneous presence of positive, negative, and cognitive symptoms that affect all aspects of mental activity. We aimed to describe the genetics of schizophrenia to widening our understanding of the inheritance of this illness.
Methods: This quasi-experimental study was conducted in Razi psychiatric hospital in Tehran province, Iran. Recruitment of the study samples was conducted in Tehran, Iran, among patients with schizophrenia and their families. For this purpose, individuals with schizophrenia in 40 families with at least 1 to 2 affected members were identified and selected based on a clinical interview conducted by a psychiatrist and according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition. The clinical and paraclinical data, drug and substance usage, and medical treatments were collected through a standardized clinical questionnaire. Besides, the Global Assessment Scale and the Positive and Negative Syndrome Scale were completed for all study participants. Results: A total of 22 families had a negative family history, and 1 affected member and the rest of the studied families had a positive family history and at least 2 affected members. In addition, genealogical data (family tree) and lymphoblastic cell categories were developed to examine genes, and subsequent research results will be reported in the future. Conclusion: As the research continues, the approach to sampling must be modified to ensure that the deoxyribonucleic acid bank is as extensively representative as possible of all schizophrenia cases.
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Affiliation(s)
- Gita Sadighi
- Department of Psychiatry, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Ali Nazeri Astaneh
- Psychosis Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohammad Reza Khodaei Ardakani
- Social Determinants of Health Research Center & Department of Psychiatry, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Saeid Latifi-Navid
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
- Corresponding author: Dr Saeid Latifi-Navid,
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25
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Sumathipala D, Strømme P, Fattahi Z, Lüders T, Sheng Y, Kahrizi K, Einarsen IH, Sloan JL, Najmabadi H, van den Heuvel L, Wevers RA, Guerrero-Castillo S, Mørkrid L, Valayannopoulos V, Backe PH, Venditti CP, van Karnebeek CD, Nilsen H, Frengen E, Misceo D. ZBTB11 dysfunction: spectrum of brain abnormalities, biochemical signature and cellular consequences. Brain 2022; 145:2602-2616. [PMID: 35104841 PMCID: PMC9337812 DOI: 10.1093/brain/awac034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022] Open
Abstract
Bi-allelic pathogenic variants in ZBTB11 have been associated with intellectual developmental disorder, autosomal recessive 69 (MRT69; OMIM 618383). We report five patients from three families with novel, bi-allelic variants in ZBTB11. We have expanded the clinical phenotype of MRT69, documenting varied severity of atrophy affecting different brain regions and described combined malonic and methylmalonic aciduria as a biochemical manifestation. As ZBTB11 encodes for a transcriptional regulator, we performeded chromatin immunoprecipitation-sequencing targeting ZBTB11 in fibroblasts from patients and controls. Chromatin immunoprecipitation-sequencing revealed binding of wild-type ZBTB11 to promoters in 238 genes, among which genes encoding proteins involved in mitochondrial functions and RNA processing are over-represented. Mutated ZBTB11 showed reduced binding to 61 of the targeted genes, indicating that the variants act as loss of function. Most of these genes are related to mitochondrial functions. Transcriptome analysis of the patient fibroblasts revealed dysregulation of mitochondrial functions. In addition, we uncovered that reduced binding of the mutated ZBTB11 to ACSF3 leads to decreased ACSF3 transcript level, explaining combined malonic and methylmalonic aciduria. Collectively, these results expand the clinical spectrum of ZBTB11-related neurological disease and give insight into the pathophysiology in which the dysfunctional ZBTB11 affect mitochondrial functions and RNA processing contributing to the neurological and biochemical phenotypes.
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Affiliation(s)
| | | | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Torben Lüders
- Department of Clinical Molecular Biology, Section of Clinical Molecular Biology (EpiGen), University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Ingunn Holm Einarsen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Jennifer L Sloan
- Organic Acid Research Section, Medical Genomics and Metabolic Genetics Branch, NHGRI, NIH, Bethesda, MD, USA
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Lambert van den Heuvel
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ron A Wevers
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands,United for Metabolic Disease—UMD, The Netherlands
| | - Sergio Guerrero-Castillo
- University Children’s Research@Kinder-UKE, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Lars Mørkrid
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Paul Hoff Backe
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Charles P Venditti
- Organic Acid Research Section, Medical Genomics and Metabolic Genetics Branch, NHGRI, NIH, Bethesda, MD, USA
| | - Clara D van Karnebeek
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands,United for Metabolic Disease—UMD, The Netherlands,Department of Pediatrics, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Section of Clinical Molecular Biology (EpiGen), University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | | | - Doriana Misceo
- Correspondence to: Doriana Misceo Department of Medical Genetics Oslo University Hospital and University of Oslo Postboks 4956 Nydalen, 0424 Oslo, Norway E-mail:
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26
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Hashemieh M, Saadatmandi ZAS, Azarkeivan A, Najmabadi H. The Effect of Xmn -1 Polymorphism and Coinheritance of Alpha Mutations on Age at First Blood Transfusion in Iranian Patients with Homozygote IVSI-5 Mutation. Int J Hematol Oncol Stem Cell Res 2022; 16:47-54. [PMID: 35975115 PMCID: PMC9339124 DOI: 10.18502/ijhoscr.v16i1.8441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 05/01/2021] [Indexed: 11/24/2022] Open
Abstract
Background: Thalassemia syndromes are the most prevalent hereditary hemoglobinopathies in the world. Iran is located on the thalassemia belt. In this study, the effect of Xmn -1 polymorphism and coinheritance of alpha mutations on age at first transfusion and also transfusion interval in Iranian thalassemic patients with homozygous IVSI-5 mutation were assessed. Materials and Methods: In this retrospective cross-sectional study 154 transfusion dependent thalassemia (TDT) patients (140 patients with β-thalassemia major and 14 cases with β-thalassemia intermedia) who were homozygote of IVSI-5 mutation have been participated. Blood samples were collected from participants using EDTA containers for genomic DNA analysis. DNA extraction and amplification-refractory mutation to determine the Xmn -1 polymorphism were performed. Multiplex PCR was performed to identify alpha globin deletions. Results: The mean age of participants was 29±7, 58 of them were male and 96 were female. A significant relation between presence of Xmn -1 polymorphism and age at receiving first transfusion was detected. Coinheritance of alpha thalassemia mutation does not have significant effect on age at first transfusion or transfusion interval. Conclusion: Presence of Xmn -1 polymorphism can delay the onset of transfusion in patients with homozygote IVSI-5 mutation.
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Affiliation(s)
- Mozhgan Hashemieh
- Department of Pediatric Hematology Oncology, Imam Hossein Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Al Sadat Saadatmandi
- Department of Pediatric Hematology Oncology, Imam Hossein Medical Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azita Azarkeivan
- Iranian Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Thalassemia Clinic, Tehran, Iran
| | - Hossein Najmabadi
- Kariminejad-Najmabadi Genetics Center, Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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27
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Goodarzi A, Rad F, Esmaeili OS, Forouzeshpour F, Najmabadi H, Azarkeivan A. 3091 – CLINICAL FEATURES AND MOLECULAR BASIS OF THALASSEMIC PATIENTS WITH HOMOZYGOTE FORM OF IVSII-I/ IVSII-I MUTATION AND SYNCHRONIZATION WITH Α-GENE MUTATION. Exp Hematol 2022. [DOI: 10.1016/j.exphem.2022.07.147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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28
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Rashvand Z, Kahrizi K, Najmabadi H, Najafipour R, Omrani MD. A novel variant of C12orf4 linked to autosomal recessive intellectual disability type 66 with phenotype expansion. J Gene Med 2021; 24:e3406. [PMID: 34967075 DOI: 10.1002/jgm.3406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 12/05/2021] [Accepted: 12/08/2021] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Intellectual disability (ID) is a hallmark of many rare disorders that are highly heterogeneous and complex. A large number of specific genes are involved in development of this heterogeneity, and each of these genes is only found in a small number of patients. This weakens the definition of the predominant genotype and the phenotypic characteristics associated with that gene. Autosomal recessive ID type 66 (OMIM # 618221) is one of these very rare diseases created by defects in C12orf4 gene. METHODS The researchers in the current study included two patients from an Iranian family with initial diagnosis of non-syndromic ID to identify the possible genetic cause(s), and whole-exome sequencing (WES) was performed for the proband. The obtained variant was confirmed by Sanger sequencing and co-segregated in the family. RESULT The patients carried a novel pathogenic splicing variant called c.1441-1G>A in exon 12 of C12orf4 gene (NM_001304811). They predominantly manifested ID, behavioral problems, speech impairment, and dysmorphic facial features, some of which had not been reported in previous studies. CONCLUSION A novel pathogenic splicing variant was identified named c.1441-1G>A in C12orf4 gene. So far, only seven families have been reported with defects in this gene. Previous studies have not highlighted the exact clinical manifestations of these patients, thus, this study could contribute to better delineation of the genotype-phenotype correlation and interpretation of very rare variants of the gene.
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Affiliation(s)
- Zahra Rashvand
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Najafipour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Averdunk L, Sticht H, Surowy H, Lüdecke HJ, Koch-Hogrebe M, Alsaif HS, Kahrizi K, Alzaidan H, Alawam BS, Tohary M, Kraus C, Endele S, Wadman E, Kaplan JD, Efthymiou S, Najmabadi H, Reis A, Alkuraya FS, Wieczorek D. The recurrent missense mutation p.(Arg367Trp) in YARS1 causes a distinct neurodevelopmental phenotype. J Mol Med (Berl) 2021; 99:1755-1768. [PMID: 34536092 PMCID: PMC8599376 DOI: 10.1007/s00109-021-02124-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 07/21/2021] [Accepted: 07/30/2021] [Indexed: 11/14/2022]
Abstract
Pathogenic variants in aminoacyl-tRNA synthetases (ARS1) cause a diverse spectrum of autosomal recessive disorders. Tyrosyl tRNA synthetase (TyrRS) is encoded by YARS1 (cytosolic, OMIM*603,623) and is responsible of coupling tyrosine to its specific tRNA. Next to the enzymatic domain, TyrRS has two additional functional domains (N-Terminal TyrRSMini and C-terminal EMAP-II-like domain) which confer cytokine-like functions. Mutations in YARS1 have been associated with autosomal-dominant Charcot-Marie-Tooth (CMT) neuropathy type C and a heterogenous group of autosomal recessive, multisystem diseases. We identified 12 individuals from 6 families with the recurrent homozygous missense variant c.1099C > T;p.(Arg367Trp) (NM_003680.3) in YARS1. This variant causes a multisystem disorder with developmental delay, microcephaly, failure to thrive, short stature, muscular hypotonia, ataxia, brain anomalies, microcytic anemia, hepatomegaly, and hypothyroidism. In silico analyses show that the p.(Arg367Trp) does not affect the catalytic domain responsible of enzymatic coupling, but destabilizes the cytokine-like C-terminal domain. The phenotype associated with p.(Arg367Trp) is distinct from the other biallelic pathogenic variants that reside in different functional domains of TyrRS which all show some common, but also divergent clinical signs [(e.g., p.(Phe269Ser)-retinal anomalies, p.(Pro213Leu)/p.(Gly525Arg)-mild ID, p.(Pro167Thr)-high fatality)]. The diverse clinical spectrum of ARS1-associated disorders is related to mutations affecting the various non-canonical domains of ARS1, and impaired protein translation is likely not the exclusive disease-causing mechanism of YARS1- and ARS1-associated neurodevelopmental disorders. KEY MESSAGES: The missense variant p.(Arg367Trp) in YARS1 causes a distinct multisystem disorder. p.(Arg367Trp) affects a non-canonical domain with cytokine-like functions. Phenotypic heterogeneity associates with the different affected YARS1 domains. Impaired protein translation is likely not the exclusive mechanism of ARS1-associated disorders.
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Affiliation(s)
- Luisa Averdunk
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University, Düsseldorf, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Harald Surowy
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Hermann-Josef Lüdecke
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | | | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hamad Alzaidan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Bashayer S Alawam
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohamed Tohary
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Cornelia Kraus
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sabine Endele
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Erin Wadman
- Division of Medical Genetics, Department of Pediatrics, Nemours Alfred I, DuPont Hospital for Children, Wilmington, Delaware, DE, USA
| | - Julie D Kaplan
- Division of Medical Genetics, Department of Pediatrics, Nemours Alfred I, DuPont Hospital for Children, Wilmington, Delaware, DE, USA
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Hossein Najmabadi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - André Reis
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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30
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Averdunk L, Sticht H, Surowy H, Lüdecke HJ, Koch-Hogrebe M, Alsaif HS, Kahrizi K, Alzaidan H, Alawam BS, Tohary M, Kraus C, Endele S, Wadman E, Kaplan JD, Efthymiou S, Najmabadi H, Reis A, Alkuraya FS, Wieczorek D. Correction to: The recurrent missense mutation p.(Arg367Trp) in YARS1 causes a distinct neurodevelopmental phenotype. J Mol Med (Berl) 2021; 99:1769-1770. [PMID: 34661688 DOI: 10.1007/s00109-021-02153-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Luisa Averdunk
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University, Düsseldorf, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Harald Surowy
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Hermann-Josef Lüdecke
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | | | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hamad Alzaidan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Bashayer S Alawam
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mohamed Tohary
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Cornelia Kraus
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sabine Endele
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Erin Wadman
- Division of Medical Genetics, Department of Pediatrics, DuPont Hospital for Children, Nemours Alfred I, Wilmington, Delaware, DE, USA
| | - Julie D Kaplan
- Division of Medical Genetics, Department of Pediatrics, DuPont Hospital for Children, Nemours Alfred I, Wilmington, Delaware, DE, USA
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Hossein Najmabadi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - André Reis
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany.
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31
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Cheraghi S, Moghbelinejad S, Najmabadi H, Kahrizi K, Najafipour R. The PTRHD1 Mutation in Intellectual Disability. Arch Iran Med 2021; 24:747-751. [PMID: 34816696 DOI: 10.34172/aim.2021.110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 02/20/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Intellectual disability (ID) is a heterogonous disorder with complex etiology. The frequency of autosomal recessive inheritance defects was elevated in a consanguineous family. METHODS In this study, high-throughput DNA sequencing was performed in an Iranian consanguineous family with two affected individuals to find potential causative variants. Whole-exome sequencing was carried out on the proband and Sanger sequencing was implemented for validation of the likely causative variant in the family members. RESULTS A novel homozygous missense mutation (p.Arg122Trp) was detected in the PTRHD1 gene. CONCLUSION PTRHD1 has been recently introduced as a candidate ID and Parkinsonism causing gene. Our findings are in agreement with the clinical spectrum of PTRHD1 mutations; however, our affected individuals suffer from ID manifestations.
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Affiliation(s)
- Sara Cheraghi
- Department of Molecular Medicine, Faculty of Medical Sciences, Qazvin University of Medical Sciences, Qazvin, Iran
- Student Research Committee, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sahar Moghbelinejad
- Cellular and Molecular Research Centre, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Najafipour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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32
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Mohseni M, Babanejad M, Booth KT, Jamali P, Jalalvand K, Davarnia B, Ardalani F, Khoshaeen A, Arzhangi S, Ghodratpour F, Beheshtian M, Jahanshad F, Otukesh H, Bahrami F, Seifati SM, Bazazzadegan N, Habibi F, Behravan H, Mirzaei S, Keshavarzi F, Nikzat N, Mehrjoo Z, Thiele H, Nothnagel M, Azaiez H, Smith RJ, Kahrizi K, Najmabadi H. Exome sequencing utility in defining the genetic landscape of hearing loss and novel-gene discovery in Iran. Clin Genet 2021; 100:59-78. [PMID: 33713422 PMCID: PMC8195868 DOI: 10.1111/cge.13956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 03/03/2021] [Accepted: 03/08/2021] [Indexed: 12/22/2022]
Abstract
Hearing loss (HL) is one of the most common sensory defects affecting more than 466 million individuals worldwide. It is clinically and genetically heterogeneous with over 120 genes causing non-syndromic HL identified to date. Here, we performed exome sequencing (ES) on a cohort of Iranian families with no disease-causing variants in known deafness-associated genes after screening with a targeted gene panel. We identified likely causal variants in 20 out of 71 families screened. Fifteen families segregated variants in known deafness-associated genes. Eight families segregated variants in novel candidate genes for HL: DBH, TOP3A, COX18, USP31, TCF19, SCP2, TENM1, and CARMIL1. In the three of these families, intrafamilial locus heterogeneity was observed with variants in both known and novel candidate genes. In aggregate, we were able to identify the underlying genetic cause of HL in nearly 30% of our study cohort using ES. This study corroborates the observation that high-throughput DNA sequencing in populations with high rates of consanguineous marriages represents a more appropriate strategy to elucidate the genetic etiology of heterogeneous conditions such as HL.
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Affiliation(s)
- Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Harvard Medical School, Department of Neurobiology, Boston, Massachusetts, USA
| | - Payman Jamali
- Shahrood Genetic Counseling Center, Welfare Organization, Semnan, Iran
| | - Khadijeh Jalalvand
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Behzad Davarnia
- Department of Anatomy and Pathology, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Fariba Ardalani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Ghodratpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Hasan Otukesh
- Department of Pediatric Neurology, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Bahrami
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Seyed Morteza Seifati
- Medical Biotechnology Research Center, Islamic Azad University, Ashkezar, Yazd, Iran
| | - Niloofar Bazazzadegan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Farkhondeh Habibi
- Genetic Counseling Center of Welfare Organization, Rasht, Guilan, Iran
| | - Hanieh Behravan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sepide Mirzaei
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Keshavarzi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Nooshin Nikzat
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Mehrjoo
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Holger Thiele
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Michael Nothnagel
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- University Hospital Cologne, Cologne, Germany
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Richard J Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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33
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Atroshi SD, Al-Allawi N, Chui DHK, Najmabadi H, Khailany RA. A Novel β 0-Thalassemia Mutation, HBB: c.356_357delTT [Codon 118 (-TT)] in an Iraqi Kurd. Hemoglobin 2021; 45:212-214. [PMID: 34167424 DOI: 10.1080/03630269.2021.1941082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
We report a novel frameshift β-thalassemia (β-thal) mutation due to a two-nucleotide deletion at codon 118 of the β-globin gene (HBB: c.356_357delTT) in a 4-year-old Iraqi Kurd female presenting as transfusion-dependent β-thal. This frameshift mutation, unlike many others involving the third exon, behaved as a recessive β0 defect and not as dominant β-thal mutation.
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Affiliation(s)
- Sulav D Atroshi
- Department of Pathology, College of Medicine, University of Duhok, Duhok, Iraq
| | - Nasir Al-Allawi
- Department of Pathology, College of Medicine, University of Duhok, Duhok, Iraq
| | - David H K Chui
- Departments of Medicine, Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Hossein Najmabadi
- Department of Genetics, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Rozhgar A Khailany
- Department of Biology, College of Science, University of Salahaddin, Erbil, Iraq
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34
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Khoshbakht S, Beheshtian M, Fattahi Z, Bazazzadegan N, Parsimehr E, Fadaee M, Vazehan R, Faraji Zonooz M, Abolhassani A, Makvand M, Kariminejad A, Celik A, Kahrizi K, Najmabadi H. CEP104 and CEP290; Genes with Ciliary Functions Cause Intellectual Disability in Multiple Families. Arch Iran Med 2021; 24:364-373. [PMID: 34196201 DOI: 10.34172/aim.2021.53] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/13/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND Neurodevelopmental and intellectual impairments are extremely heterogeneous disorders caused by a diverse variety of genes involved in different molecular pathways and networks. Genetic alterations in cilia, highly-conserved organelles with sensorineural and signal transduction roles can compromise their proper functions and lead to so-called "ciliopathies" featuring intellectual disability (ID) or neurodevelopmental disorders as frequent clinical manifestations. Here, we report several Iranian families affected with ID and other ciliopathy-associated features carrying known and novel variants in two ciliary genes; CEP104 and CEP290. METHODS Whole exome and Targeted exome sequencing were carried out on affected individuals. Lymphoblastoid cell lines (LCLs) derived from the members of affected families were established for two families carrying CEP104 mutations. RNA and protein expression studies were carried out on these cells using qPCR and Western blot, respectively. RESULTS A novel homozygous variant; NM_025114.3:c.7341_7344dupACTT p.(Ser2449Thrfs*8) and four previously reported homozygous variants; NM_025114.3:c.322C>T p.(Arg108*), NM_025114.3:c.4393C>T p.(Arg1465*), NM_025114.3:c.5668G>T p.(Gly1890*) and NM_025114.3:c.1666dupA p.(Ile556Asnfs*20) were identified in CEP290. In two other families, two novel homozygous variants; NM_014704:c.2356_2357insTT p.(Cys786Phefs*11) and NM_014704:c.1901_1902insT p.(Leu634Phefs*33) were identified in CEP104, another ciliary gene. qPCR and Western blot analyses showed significantly lower levels of CEP104 transcripts and protein in patients compared to heterozygous or normal family members. CONCLUSION We emphasize on the clinical variability and pleiotropic phenotypes due to variants of these genes. In conclusion, our findings support the pivotal role of these genes resulting in cognitive and neurodevelopmental features.
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Affiliation(s)
- Shahrouz Khoshbakht
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Niloofar Bazazzadegan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Elham Parsimehr
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Mahsa Fadaee
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Raheleh Vazehan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Ayda Abolhassani
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Mina Makvand
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Arzu Celik
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
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35
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Fattahi Z, Mohseni M, Jalalvand K, Aghakhani Moghadam F, Ghaziasadi A, Keshavarzi F, Yavarian J, Jafarpour A, Mortazavi SE, Ghodratpour F, Behravan H, Khazeni M, Momeni SA, Jahanzad I, Moradi A, Tabarraei A, Azimi SA, Kord E, Hashemi-Shahri SM, Azaran A, Yousefi F, Mokhames Z, Soleimani A, Ghafari S, Ziaee M, Habibzadeh S, Jeddi F, Hadadi A, Abdollahi A, Kaydani GA, Soltani S, Mokhtari-Azad T, Najafipour R, Malekzadeh R, Kahrizi K, Jazayeri SM, Najmabadi H. SARS-CoV-2 outbreak in Iran: The dynamics of the epidemic and evidence on two independent introductions. Transbound Emerg Dis 2021; 69:1375-1386. [PMID: 33835709 PMCID: PMC8251331 DOI: 10.1111/tbed.14104] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/27/2022]
Abstract
The SARS‐CoV‐2 virus has been rapidly spreading globally since December 2019, triggering a pandemic, soon after its emergence. While Iran was among the first countries confronted with rapid spread of virus in February 2020, no real‐time SARS‐CoV‐2 whole‐genome tracking in early phase of outbreak was performed in the country. To address this issue, we provided 50 whole‐genome sequences of viral isolates ascertained from different geographical locations in Iran during March–July 2020. The corresponding analysis on origins, transmission dynamics and genetic diversity of SARS‐CoV‐2 virus, represented at least two introductions of the virus into the country, constructing two major clusters defined as B.4 and B.1*. The first entry of the virus might have occurred around very late 2019/early 2020, as suggested by the time to the most recent common ancestor, followed by a rapid community transmission that led to dominancy of B.4 lineage in early epidemic till the end of June. Gradually, reduction in dominancy of B.4 occurred possibly as a result of other entries of the virus, followed by surge of B.1* lineages, as of mid‐May. Remarkably, variation tracking of the virus indicated the increase in frequency of D614G mutation, along with B.1* lineages, which showed continuity till October 2020. The increase in frequency of D614G mutation and B.1* lineages from mid‐May onwards predicts a rapid viral transmission that may push the country into a critical health situation followed by a considerable change in composition of viral lineages circulating in the country.
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Affiliation(s)
- Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran.,Student Research Committee, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Jalalvand
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Azam Ghaziasadi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Keshavarzi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Jila Yavarian
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Jafarpour
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyedeh Elham Mortazavi
- Department of Microbiology, Faculty of Biology, College of Science, University of Science & Research, Tehran, Iran
| | - Fatemeh Ghodratpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hanieh Behravan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohammad Khazeni
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Booali Laboratory, Qom, Iran
| | | | | | - Abdolvahab Moradi
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Golestan, Iran
| | - Alijan Tabarraei
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Golestan, Iran
| | - Sadegh Ali Azimi
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Golestan, Iran
| | - Ebrahim Kord
- Infectious Disease and Tropical Medicine Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Seyed Mohammad Hashemi-Shahri
- Infectious Disease and Tropical Medicine Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Azarakhsh Azaran
- Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farid Yousefi
- Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Zakiye Mokhames
- Department of Molecular Diagnostic, Emam Ali Educational and Therapeutic Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Alireza Soleimani
- Department of Molecular Diagnostic, Emam Ali Educational and Therapeutic Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Shokouh Ghafari
- Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Masood Ziaee
- Infectious Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Shahram Habibzadeh
- Department of Infectious Disease, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Farhad Jeddi
- Department of Infectious Disease, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Azar Hadadi
- Department of Infectious Disease, School of Medicine, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Abdollahi
- Department of Pathology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholam Abbas Kaydani
- Department of Laboratory Sciences, School of Allied Medical Sciences, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Saber Soltani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Talat Mokhtari-Azad
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Najafipour
- Cell and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Reza Malekzadeh
- Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Seyed Mohammad Jazayeri
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
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36
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Nair D, Li D, Erdogan H, Yoon A, Harr MH, Bergant G, Peterlin B, Škrjanec Pušenjak M, Jayakar P, Pfundt R, Jansen S, McWalter K, Sidhu A, Saliganan S, Agolini E, Jacob A, Pasquier J, Arash R, Kahrizi K, Najmabadi H, Ropers HH, Bhoj EJ. Discovery of a neuromuscular syndrome caused by biallelic variants in ASCC3. Human Genetics and Genomics Advances 2021; 2:100024. [PMID: 35047834 PMCID: PMC8756546 DOI: 10.1016/j.xhgg.2021.100024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/13/2021] [Indexed: 11/11/2022] Open
Abstract
Activating Signal Cointegrator 1 Complex, Subunit 3 (ASCC3) is part of the four-part ASC-1 transcriptional cointegrator complex. This complex includes ASCC1 (associated with spinal muscular atrophy with congenital bone fractures 2), TRIP4 (associated with spinal muscular atrophy with congenital bone fractures 1), and ASCC2 (not yet associated with human disease.) ASCC3 encodes a DNA helicase responsible for generating single-stranded DNA as part of the DNA damage response. Interestingly, ASCC3 expresses coding and non-coding isoforms, which act in opposition to balance the recovery of gene transcription after UV-induced DNA damage. Here we report the discovery of ASCC3 as the cause of a neuromuscular syndrome in seven unreported individuals from six unrelated families and updates on the one previously reported family. All the individuals share a neurologic phenotype that ranges from severe developmental delay to muscle fatigue. There appears to be genotype-phenotype correlation, as the most mildly affected individual is homozygous for a rare missense variant, while the more severely affected individuals are compound heterozygotes for a missense and a presumed loss-of-function (LOF) variant. There are no individuals with biallelic presumed LOF variants in our cohort or in gnomAD, as this genotype may not be compatible with life. In summary we report a syndrome in these eleven individuals from seven families with biallelic variants in ASCC3.
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37
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Najafi K, Mehrjoo Z, Ardalani F, Ghaderi-Sohi S, Kariminejad A, Kariminejad R, Najmabadi H. Identifying the causes of recurrent pregnancy loss in consanguineous couples using whole exome sequencing on the products of miscarriage with no chromosomal abnormalities. Sci Rep 2021; 11:6952. [PMID: 33772059 PMCID: PMC7997959 DOI: 10.1038/s41598-021-86309-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/08/2021] [Indexed: 12/26/2022] Open
Abstract
Recurrent miscarriages occur in about 5% of couples trying to conceive. In the past decade, the products of miscarriage have been studied using array comparative genomic hybridization (a-CGH). Within the last decade, an association has been proposed between miscarriages and single or multigenic changes, introducing the possibility of detecting other underlying genetic factors by whole exome sequencing (WES). We performed a-CGH on the products of miscarriage from 1625 Iranian women in consanguineous or non-consanguineous marriages. WES was carried out on DNA extracted from the products of miscarriage from 20 Iranian women in consanguineous marriages and with earlier normal genetic testing. Using a-CGH, a statistically significant difference was detected between the frequency of imbalances in related vs. unrelated couples (P < 0.001). WES positively identified relevant alterations in 11 genes in 65% of cases. In 45% of cases, we were able to classify these variants as pathogenic or likely pathogenic, according to the American College of Medical Genetics and Genomics guidelines, while in the remainder, the variants were classified as of unknown significance. To the best of our knowledge, our study is the first to employ WES on the products of miscarriage in consanguineous families with recurrent miscarriages regardless of the presence of fetal abnormalities. We propose that WES can be helpful in making a diagnosis of lethal disorders in consanguineous couples after prior genetic testing.
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Affiliation(s)
- Kimia Najafi
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Zohreh Mehrjoo
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran
| | - Fariba Ardalani
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran
| | - Siavash Ghaderi-Sohi
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Ariana Kariminejad
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Roxana Kariminejad
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran
| | - Hossein Najmabadi
- Genetic Research Center, National Reference Laboratory for Prenatal Diagnosis, University of Social Welfare and Rehabilitation Sciences, Koodakyar Avenue, Daneshjoo Blvd, Evin, Tehran, 1985713834, Iran.
- Kariminejad-Najmabadi Pathology and Genetics Center, #2, West Side of Sanat Sq.-Metro Station, Shahrak Gharb, Tehran, 1466713713, Iran.
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38
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Rashvand Z, Kahrizi K, Najmabadi H, Najafipour R, Omrani MD. Clinical and Genetic Characteristics of Splicing Variant in CYP27A1 in an Iranian Family with Cerebrotendinous Xanthomatosis. Iran Biomed J 2021; 25:132-9. [PMID: 33400472 PMCID: PMC7921520 DOI: 10.29252/ibj.25.2.132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Background: CTX is a rare congenital lipid-storage disorder, leading to a progressive multisystem disease. CTX with autosomal recessive inheritance is caused by a defect in the CYP27A1 gene. Chronic diarrhea, tendon xanthomas, neurologic impairment, and bilateral cataracts are common symptoms of the disease. Methods: Three affected siblings with an initial diagnosis of non-syndromic intellectual disability were recruited for further molecular investigations. To identify the possible genetic cause(s), WES was performed on the proband. Sanger sequencing was applied to confirm the final variant. The clinical and molecular genetic features of the three siblings from the new CTX family and other patients with the same mutations, as previously reported, were analyzed. The CYP27A1 gene was also studied for the number of pathogenic variants and their location. Results: We found a homozygous splicing mutation, NM_000784: exon6: c.1184+1G>A, in CYP27A1 gene, which was confirmed by Sanger sequencing. Among the detected pathogenic variants, the splice site mutation had the highest prevalence, and the mutations were mostly found in exon 4. Conclusion: This study is the first to report the c.1184+1G>A mutation in Iran. Our findings highlight the other feature of the disease, which is the lack of relationship between phenotype and genotype. Due to nonspecific symptoms and delay in diagnosis, CYP27A1 genetic analysis should be the definitive method for CTX diagnosis.
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Affiliation(s)
- Zahra Rashvand
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Najafipour
- Cellular and Molecular Research Centre, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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39
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Diaz J, Gérard X, Emerit MB, Areias J, Geny D, Dégardin J, Simonutti M, Guerquin MJ, Collin T, Viollet C, Billard JM, Métin C, Hubert L, Larti F, Kahrizi K, Jobling R, Agolini E, Shaheen R, Zigler A, Rouiller-Fabre V, Rozet JM, Picaud S, Novelli A, Alameer S, Najmabadi H, Cohn R, Munnich A, Barth M, Lugli L, Alkuraya FS, Blaser S, Gashlan M, Besmond C, Darmon M, Masson J. YIF1B mutations cause a post-natal neurodevelopmental syndrome associated with Golgi and primary cilium alterations. Brain 2021; 143:2911-2928. [PMID: 33103737 DOI: 10.1093/brain/awaa235] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/29/2020] [Accepted: 06/13/2020] [Indexed: 12/30/2022] Open
Abstract
Human post-natal neurodevelopmental delay is often associated with cerebral alterations that can lead, by themselves or associated with peripheral deficits, to premature death. Here, we report the clinical features of 10 patients from six independent families with mutations in the autosomal YIF1B gene encoding a ubiquitous protein involved in anterograde traffic from the endoplasmic reticulum to the cell membrane, and in Golgi apparatus morphology. The patients displayed global developmental delay, motor delay, visual deficits with brain MRI evidence of ventricle enlargement, myelination alterations and cerebellar atrophy. A similar profile was observed in the Yif1b knockout (KO) mouse model developed to identify the cellular alterations involved in the clinical defects. In the CNS, mice lacking Yif1b displayed neuronal reduction, altered myelination of the motor cortex, cerebellar atrophy, enlargement of the ventricles, and subcellular alterations of endoplasmic reticulum and Golgi apparatus compartments. Remarkably, although YIF1B was not detected in primary cilia, biallelic YIF1B mutations caused primary cilia abnormalities in skin fibroblasts from both patients and Yif1b-KO mice, and in ciliary architectural components in the Yif1b-KO brain. Consequently, our findings identify YIF1B as an essential gene in early post-natal development in human, and provide a new genetic target that should be tested in patients developing a neurodevelopmental delay during the first year of life. Thus, our work is the first description of a functional deficit linking Golgipathies and ciliopathies, diseases so far associated exclusively to mutations in genes coding for proteins expressed within the primary cilium or related ultrastructures. We therefore propose that these pathologies should be considered as belonging to a larger class of neurodevelopmental diseases depending on proteins involved in the trafficking of proteins towards specific cell membrane compartments.
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Affiliation(s)
- Jorge Diaz
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France
| | - Xavier Gérard
- INSERM UMR-S1163 Imagine Institute for Genetic Diseases, Paris Descartes-Sorbonne Paris Cité University, France
| | - Michel-Boris Emerit
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France
| | - Julie Areias
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France
| | - David Geny
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France
| | - Julie Dégardin
- INSERM UMR-S968, Institut de la vision, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris F-75012, Université Pierre et Marie Curie, France
| | - Manuel Simonutti
- INSERM UMR-S968, Institut de la vision, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris F-75012, Université Pierre et Marie Curie, France
| | | | - Thibault Collin
- Saint Pères Paris Institute for the Neurosciences CNRS - UMR 8003 Université de Paris, Paris 75006, France
| | - Cécile Viollet
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France
| | - Jean-Marie Billard
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France
| | - Christine Métin
- INSERM, UMR-S1270, Institut du Fer à Moulin, Sorbonne Université, Paris F-75005, France
| | - Laurence Hubert
- INSERM UMR-S1163 Imagine Institute for Genetic Diseases, Paris Descartes-Sorbonne Paris Cité University, France
| | - Farzaneh Larti
- University of Social Welfare and Rehabilitation Sciences, Genetics Research Center, Tehran 19834, Iran
| | - Kimia Kahrizi
- University of Social Welfare and Rehabilitation Sciences, Genetics Research Center, Tehran 19834, Iran
| | - Rebekah Jobling
- The Hospital for Sick Children, Molecular Genetics, Toronto, Canada
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, 00146 Rome, Italy
| | - Ranad Shaheen
- King Faisal Specialist Hospital and Research Center, Developmental Genetics Unit, Riyadh 11211, Saudi Arabia
| | | | | | - Jean-Michel Rozet
- INSERM UMR-S1163 Imagine Institute for Genetic Diseases, Paris Descartes-Sorbonne Paris Cité University, France
| | - Serge Picaud
- INSERM UMR-S968, Institut de la vision, Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Paris F-75012, Université Pierre et Marie Curie, France
| | - Antonio Novelli
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, 00146 Rome, Italy
| | - Seham Alameer
- Department of Pediatrics, King Khaled National Guard Hospital, King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Hossein Najmabadi
- University of Social Welfare and Rehabilitation Sciences, Genetics Research Center, Tehran 19834, Iran
| | - Ronald Cohn
- The Hospital for Sick Children, Molecular Genetics, Toronto, Canada
| | - Arnold Munnich
- INSERM UMR-S1163 Imagine Institute for Genetic Diseases, Paris Descartes-Sorbonne Paris Cité University, France
| | | | - Licia Lugli
- Division of Neonatal Intensive Care Unit, Department of Pediatrics, University Hospital, 41125 Modena, Italy
| | - Fowzan S Alkuraya
- King Faisal Specialist Hospital and Research Center, Developmental Genetics Unit, Riyadh 11211, Saudi Arabia
| | - Susan Blaser
- Division of Neuroradiology, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Maha Gashlan
- King Faisal Specialist Hospital and Research Center, Developmental Genetics Unit, Riyadh 11211, Saudi Arabia
| | - Claude Besmond
- INSERM UMR-S1163 Imagine Institute for Genetic Diseases, Paris Descartes-Sorbonne Paris Cité University, France
| | - Michèle Darmon
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France.,INSERM, UMR-S1270, Institut du Fer à Moulin, Sorbonne Université, Paris F-75005, France
| | - Justine Masson
- INSERM UMR894, Center for Psychiatry and Neuroscience, Paris F-75014, Université Paris Descartes, Sorbonne Paris Cité - Paris 5, France.,INSERM, UMR-S1270, Institut du Fer à Moulin, Sorbonne Université, Paris F-75005, France
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40
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Jonkhout N, Cruciani S, Santos Vieira HG, Tran J, Liu H, Liu G, Pickford R, Kaczorowski D, Franco GR, Vauti F, Camacho N, Abedini SS, Najmabadi H, Ribas de Pouplana L, Christ D, Schonrock N, Mattick JS, Novoa EM. Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation. RNA Biol 2021; 18:1905-1919. [PMID: 33499731 DOI: 10.1080/15476286.2021.1881291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
RNA modifications are dynamic chemical entities that expand the RNA lexicon and regulate RNA fate. The most abundant modification present in mRNAs, N6-methyladenosine (m6A), has been implicated in neurogenesis and memory formation. However, whether additional RNA modifications may be playing a role in neuronal functions and in response to environmental queues is largely unknown. Here we characterize the biochemical function and cellular dynamics of two human RNA methyltransferases previously associated with neurological dysfunction, TRMT1 and its homolog, TRMT1-like (TRMT1L). Using a combination of next-generation sequencing, LC-MS/MS, patient-derived cell lines and knockout mouse models, we confirm the previously reported dimethylguanosine (m2,2G) activity of TRMT1 in tRNAs, as well as reveal that TRMT1L, whose activity was unknown, is responsible for methylating a subset of cytosolic tRNAAla(AGC) isodecoders at position 26. Using a cellular in vitro model that mimics neuronal activation and long term potentiation, we find that both TRMT1 and TRMT1L change their subcellular localization upon neuronal activation. Specifically, we observe a major subcellular relocalization from mitochondria and other cytoplasmic domains (TRMT1) and nucleoli (TRMT1L) to different small punctate compartments in the nucleus, which are as yet uncharacterized. This phenomenon does not occur upon heat shock, suggesting that the relocalization of TRMT1 and TRMT1L is not a general reaction to stress, but rather a specific response to neuronal activation. Our results suggest that subcellular relocalization of RNA modification enzymes may play a role in neuronal plasticity and transmission of information, presumably by addressing new targets.
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Affiliation(s)
- Nicky Jonkhout
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Sonia Cruciani
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain
| | - Helaine Graziele Santos Vieira
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Julia Tran
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Huanle Liu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Ganqiang Liu
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,Current Address: School of Medicine, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, NSW, Australia
| | | | - Gloria R Franco
- Departamento De Bioquímica E Imunologia, Universidade Federal De Minas Gerais,Belo Horizonte,Minas Gerais, Brazil
| | - Franz Vauti
- Division of Cellular & Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Noelia Camacho
- Institute for Research in Biomedicine, Barcelona, Catalonia, Spain
| | - Seyedeh Sedigheh Abedini
- Department of Genetics, Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Department of Genetics, Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, Barcelona, Catalonia, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia, Spain
| | - Daniel Christ
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Nicole Schonrock
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Eva Maria Novoa
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain
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41
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Kariminejad A, Shakiba M, Shams M, Namiranian P, Eghbali M, Talebi S, Makvand M, Jaeken J, Najmabadi H, Hennekam RC. NGLY1 deficiency: Novel variants and literature review. Eur J Med Genet 2021; 64:104146. [PMID: 33497766 DOI: 10.1016/j.ejmg.2021.104146] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 12/05/2020] [Accepted: 01/20/2021] [Indexed: 01/26/2023]
Abstract
NGLY1 deficiency is a recently described autosomal recessive disorder, involved in deglycosylation of proteins, and for that reason grouped as the congenital disorders of deglycosylation together with the lysosomal storage disorders. The typical phenotype is characterized by intellectual disability, liver malfunctioning, muscular hypotonia, involuntary movements, and decreased or absent tear production. Liver biopsy demonstrates vacuolar amorphous cytoplasmic storage material. NGLY1 deficiency is caused by bi-allelic variants in NGLY1 which catalyzes protein deglycosylation. We describe five patients from two families with NGLY1 deficiency due to homozygosity for two novel NGLY1 variants, and compare their findings to those of earlier reported patients. The typical features of the disorder are present in a limited way, and there is intra-familial variability. In addition in one of the families the muscle atrophy and posture abnormalities are marked. These can be explained either as variability of the phenotype or as sign of slowly progression of features as the present affected individuals are older than earlier reported patients.
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Affiliation(s)
| | - Marjan Shakiba
- Pediatric Endocrinology and Metabolism Department, Mofid Children Hospital, Shahid Beheshti, University of Medical Science, Tehran, Iran
| | - Mehrvash Shams
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Parva Namiranian
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Maryam Eghbali
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Said Talebi
- Department of Medical Genetics and Molecular Biology, Faculty of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran.
| | - Mina Makvand
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran
| | - Jaak Jaeken
- Department of Development and Regeneration, Center for Metabolic Diseases, KU Leuven, Leuven, Belgium
| | - Hossein Najmabadi
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, Iran; Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Raoul C Hennekam
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
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42
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Neishabury M, Azarkeivan A, Mehri M, Najmabadi H, Cheraghi T. The First Case of BENTA Disease (B Cell Expansion with NF-κB and T Cell Anergy) from Iran. J Clin Immunol 2021; 41:811-813. [PMID: 33442788 PMCID: PMC7806197 DOI: 10.1007/s10875-021-00965-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/01/2021] [Indexed: 11/26/2022]
Affiliation(s)
- Maryam Neishabury
- Genetics Research Centre, University of Social Welfare and Rehabilitation Sciences, Kodakyar ave., Daneshjo Blvd., Evin, Tehran, 1985713871, Iran.
| | - Azita Azarkeivan
- Blood Transfusion Research Centre, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Maghsood Mehri
- Genetics Research Centre, University of Social Welfare and Rehabilitation Sciences, Kodakyar ave., Daneshjo Blvd., Evin, Tehran, 1985713871, Iran
| | - Hossein Najmabadi
- Genetics Research Centre, University of Social Welfare and Rehabilitation Sciences, Kodakyar ave., Daneshjo Blvd., Evin, Tehran, 1985713871, Iran
- Kariminejad-Najmabadi Pathology & Genetics Centre, Tehran, Iran
| | - Taher Cheraghi
- Department of Pediatrics, 17th Shahrivar Children's Hospital, Guilan University of Medical Sciences, Rasht, Iran.
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43
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Sheikh TI, Vasli N, Pastore S, Kharizi K, Harripaul R, Fattahi Z, Pande S, Naeem F, Hussain A, Mir A, Islam O, Girisha KM, Irfan M, Ayub M, Schwarzer C, Najmabadi H, Shukla A, Sladky VC, Braun VZ, Garcia-Carpio I, Villunger A, Vincent JB. Biallelic mutations in the death domain of PIDD1 impair caspase-2 activation and are associated with intellectual disability. Transl Psychiatry 2021; 11:1. [DOI: https:/doi.org/10.1038/s41398-020-01158-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 10/10/2023] Open
Abstract
AbstractPIDD1 encodes p53-Induced Death Domain protein 1, which acts as a sensor surveilling centrosome numbers and p53 activity in mammalian cells. Early results also suggest a role in DNA damage response where PIDD1 may act as a cell-fate switch, through interaction with RIP1 and NEMO/IKKg, activating NF-κB signaling for survival, or as an apoptosis-inducing protein by activating caspase-2. Biallelic truncating mutations in CRADD—the protein bridging PIDD1 and caspase-2—have been reported in intellectual disability (ID), and in a form of lissencephaly. Here, we identified five families with ID from Iran, Pakistan, and India, with four different biallelic mutations in PIDD1, all disrupting the Death Domain (DD), through which PIDD1 interacts with CRADD or RIP1. Nonsense mutations Gln863* and Arg637* directly disrupt the DD, as does a missense mutation, Arg815Trp. A homozygous splice mutation in the fifth family is predicted to disrupt splicing upstream of the DD, as confirmed using an exon trap. In HEK293 cells, we show that both Gln863* and Arg815Trp mutants fail to co-localize with CRADD, leading to its aggregation and mis-localization, and fail to co-precipitate CRADD. Using genome-edited cell lines, we show that these three PIDD1 mutations all cause loss of PIDDosome function. Pidd1 null mice show decreased anxiety, but no motor abnormalities. Together this indicates that PIDD1 mutations in humans may cause ID (and possibly lissencephaly) either through gain of function or secondarily, due to altered scaffolding properties, while complete loss of PIDD1, as modeled in mice, may be well tolerated or is compensated for.
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Sheikh TI, Vasli N, Pastore S, Kharizi K, Harripaul R, Fattahi Z, Pande S, Naeem F, Hussain A, Mir A, Islam O, Girisha KM, Irfan M, Ayub M, Schwarzer C, Najmabadi H, Shukla A, Sladky VC, Braun VZ, Garcia-Carpio I, Villunger A, Vincent JB. Biallelic mutations in the death domain of PIDD1 impair caspase-2 activation and are associated with intellectual disability. Transl Psychiatry 2021; 11:1. [PMID: 33414379 PMCID: PMC7791037 DOI: 10.1038/s41398-020-01158-w] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022] Open
Abstract
PIDD1 encodes p53-Induced Death Domain protein 1, which acts as a sensor surveilling centrosome numbers and p53 activity in mammalian cells. Early results also suggest a role in DNA damage response where PIDD1 may act as a cell-fate switch, through interaction with RIP1 and NEMO/IKKg, activating NF-κB signaling for survival, or as an apoptosis-inducing protein by activating caspase-2. Biallelic truncating mutations in CRADD-the protein bridging PIDD1 and caspase-2-have been reported in intellectual disability (ID), and in a form of lissencephaly. Here, we identified five families with ID from Iran, Pakistan, and India, with four different biallelic mutations in PIDD1, all disrupting the Death Domain (DD), through which PIDD1 interacts with CRADD or RIP1. Nonsense mutations Gln863* and Arg637* directly disrupt the DD, as does a missense mutation, Arg815Trp. A homozygous splice mutation in the fifth family is predicted to disrupt splicing upstream of the DD, as confirmed using an exon trap. In HEK293 cells, we show that both Gln863* and Arg815Trp mutants fail to co-localize with CRADD, leading to its aggregation and mis-localization, and fail to co-precipitate CRADD. Using genome-edited cell lines, we show that these three PIDD1 mutations all cause loss of PIDDosome function. Pidd1 null mice show decreased anxiety, but no motor abnormalities. Together this indicates that PIDD1 mutations in humans may cause ID (and possibly lissencephaly) either through gain of function or secondarily, due to altered scaffolding properties, while complete loss of PIDD1, as modeled in mice, may be well tolerated or is compensated for.
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Affiliation(s)
- Taimoor I Sheikh
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Molecular Genetics Laboratory, North York General Hosptial Genetics Program, Toronto, ON, M2K 1E1, Canada
| | - Nasim Vasli
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
| | - Stephen Pastore
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Kimia Kharizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19834, Iran
| | - Ricardo Harripaul
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19834, Iran
| | - Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Farooq Naeem
- General and Health Systems Psychiatry, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Abrar Hussain
- Human Molecular Genetics Lab, Department of Biological Sciences, FBAS, International Islamic University, Islamabad, Pakistan
| | - Asif Mir
- Human Molecular Genetics Lab, Department of Biological Sciences, FBAS, International Islamic University, Islamabad, Pakistan
| | - Omar Islam
- Department of Diagnostic Radiology, Queens University, Kingston, ON, K7L 2V7, Canada
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Muhammad Irfan
- Department of Mental Health, Psychiatry and Behavioural Sciences, Peshawar Medical College, Riphah International University, Islamabad, Pakistan
| | - Muhammad Ayub
- Lahore Institute of Research & Development, Lahore, 51000, Pakistan
- Department of Psychiatry, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Christoph Schwarzer
- Department of Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, 19834, Iran
- Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, 14667, Iran
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Valentina C Sladky
- Institute for Developmental Immunology, Biocenter Medical University of Innsbruck, Innsbruck, Austria
| | - Vincent Zoran Braun
- Institute for Developmental Immunology, Biocenter Medical University of Innsbruck, Innsbruck, Austria
| | - Irmina Garcia-Carpio
- Institute for Developmental Immunology, Biocenter Medical University of Innsbruck, Innsbruck, Austria
| | - Andreas Villunger
- Institute for Developmental Immunology, Biocenter Medical University of Innsbruck, Innsbruck, Austria.
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, M5T 1R8, Canada.
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Kazemi G, Peymani F, Mohseni M, Zare Ashrafi F, Arzhangi S, Ardalani F, Aghakhani Moghaddam F, Kahrizi K, Najmabadi H. Novel Mutation in LARP7 in Two Iranian Consanguineous Families with Syndromic Intellectual Disability and Facial Dysmorphism. Arch Iran Med 2020; 23:842-847. [PMID: 33356342 DOI: 10.34172/aim.2020.112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/20/2020] [Indexed: 11/09/2022]
Abstract
BACKGROUND Recently, we have reported mutations in LARP7 gene, leading to neurodevelopmental disorders (NDDs), the most frequent cause of disability in children with a broad phenotype spectrum and diverse genetic landscape. METHODS Here, we present two Iranian patients from consanguineous families with syndromic intellectual disability, facial dysmorphism, and short stature. RESULTS Whole-exome sequencing (WES) revealed a novel homozygous stop-gain (c.C925T, p.R309X) variant and a previously known homozygous acceptor splice-site (c.1669-1_1671del) variant in LARP7 gene, indicating the diagnosis of Alazami syndrome. CONCLUSION These identified variants in patients with Alazami syndrome were consistent with previously reported loss of function variants in LARP7 and provide further evidence that loss of function of LARP7 is the disease mechanism.
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Affiliation(s)
- Goli Kazemi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Peymani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Student Research Committee, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fariba Ardalani
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Forouzesh Pour F, Karimi K, Ghaderi Z, Tavakoli Koudehi A, Najmabadi H. Heterozygosity for the Novel HBA2: c.*91_*92delTA Polyadenylation Site Variant on the α2-Globin Gene Expanding the Genetic Spectrum of α-Thalassemia in Iran. Hemoglobin 2020; 44:423-426. [PMID: 33054440 DOI: 10.1080/03630269.2020.1831529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
There are four copy numbers of α-globin genes (16p13.3) in the human genome and the number of defective α-globin genes dictates the severity of α-thalassemia (α-thal). Mutations that occur in the 3' untranslated region (3'UTR), and especially at the polyadenylation (polyA) sites, affect the translation, stability and export of mRNA. A patient with hypochromic microcytic anemia was referred to the Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran by the health network. Molecular analysis of genomic DNA for the evaluation of mutations on the α- and β-globin genes was performed. Direct sequencing of the hemoglobin (Hb) subunit α2 (HBA2) gene revealed a two nucleotide deletion between +816 and +817 in the 3'UTR, located at the polyA site, which seems to be a novel pathogenic variant. This novel variant expands the genetic spectrum of α-thal in the 3'UTR of the HBA2 gene.
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Affiliation(s)
| | - Keyvan Karimi
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zhila Ghaderi
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Hossein Najmabadi
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran.,Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Beheshtian M, Akhtarkhavari T, Mehvari S, Mohseni M, Fattahi Z, Abedini SS, Arzhangi S, Fadaee M, Jamali P, Najafipour R, Kalscheuer VM, Hu H, Ropers HH, Najmabadi H, Kahrizi K. Comprehensive genotype-phenotype correlation in AP-4 deficiency syndrome; Adding data from a large cohort of Iranian patients. Clin Genet 2020; 99:187-192. [PMID: 32895917 DOI: 10.1111/cge.13845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/21/2020] [Accepted: 09/02/2020] [Indexed: 12/25/2022]
Abstract
Mutations in adaptor protein complex-4 (AP-4) genes have first been identified in 2009, causing a phenotype termed as AP-4 deficiency syndrome. Since then several patients with overlapping phenotypes, comprised of intellectual disability (ID) and spastic tetraplegia have been reported. To delineate the genotype-phenotype correlation of the AP-4 deficiency syndrome, we add the data from 30 affected individuals from 12 out of 640 Iranian families with ID in whom we detected disease-causing variants in AP-4 complex subunits, using next-generation sequencing. Furthermore, by comparing genotype-phenotype findings of those affected individuals with previously reported patients, we further refine the genotype-phenotype correlation in this syndrome. The most frequent reported clinical findings in the 101 cases consist of ID and/or global developmental delay (97%), speech disorders (92.1%), inability to walk (90.1%), spasticity (77.2%), and microcephaly (75.2%). Spastic tetraplegia has been reported in 72.3% of the investigated patients. The major brain imaging findings are abnormal corpus callosum morphology (63.4%) followed by ventriculomegaly (44.5%). Our result might suggest the AP-4 deficiency syndrome as a major differential diagnostic for unknown hereditary neurodegenerative disorders.
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Affiliation(s)
- Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Tara Akhtarkhavari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sepideh Mehvari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Seyedeh Sedigheh Abedini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mahsa Fadaee
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Payman Jamali
- Genetic Counseling Center, Shahroud Welfare Organization, Semnan, Iran
| | - Reza Najafipour
- Cellular and Molecular Research Centre, Genetic Department, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hao Hu
- Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Hans-Hilger Ropers
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute for Human Genetics, University Medicine, Mainz, Germany
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology and Genetics Center, Molecular division, Tehran, Islamic Republic of Iran, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Mehvari S, Larti F, Hu H, Fattahi Z, Beheshtian M, Abedini SS, Arzhangi S, Ropers HH, Kalscheuer VM, Auld D, Kahrizi K, Riazalhosseini Y, Najmabadi H. Whole genome sequencing identifies a duplicated region encompassing Xq13.2q13.3 in a large Iranian family with intellectual disability. Mol Genet Genomic Med 2020; 8:e1418. [PMID: 32715656 PMCID: PMC7549592 DOI: 10.1002/mgg3.1418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/16/2020] [Accepted: 06/29/2020] [Indexed: 12/20/2022] Open
Abstract
Background The X chromosome has historically been one of the most thoroughly investigated chromosomes regarding intellectual disability (ID), whose etiology is attributed to many factors including copy number variations (CNVs). Duplications of the long arm of the X chromosome have been reported in patients with ID, short stature, facial anomalies, and in many cases hypoplastic genitalia and/or behavioral abnormalities. Methods Here, we report on a large Iranian family with X‐linked ID caused by a duplication on the X chromosome identified by whole genome sequencing in combination with linkage analysis. Results Seven affected males in different branches of the family presented with ID, short stature, seizures, facial anomalies, behavioral abnormalities (aggressiveness, self‐injury, anxiety, impaired social interactions, and shyness), speech impairment, and micropenis. The duplication of the region Xq13.2q13.3, which is ~1.8 Mb in size, includes seven protein‐coding OMIM genes. Three of these genes, namely SLC16A2, RLIM, and NEXMIF, if impaired, can lead to syndromes presenting with ID. Of note, this duplicated region was located within a linkage interval with a LOD score >3. Conclusion Our report indicates that CNVs should be considered in multi‐affected families where no candidate gene defect has been identified in sequencing data analysis.
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Affiliation(s)
- Sepideh Mehvari
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Farzaneh Larti
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hao Hu
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Islamic Republic of Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Islamic Republic of Iran
| | - Seyedeh Sedigheh Abedini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hans-Hilger Ropers
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Human Genetics, University Medicine, Mainz, Germany
| | | | - Daniel Auld
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, Montreal, Quebec, Canada
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Yasser Riazalhosseini
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, Montreal, Quebec, Canada
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Islamic Republic of Iran
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Fatehi F, Okhovat AA, Nilipour Y, Mroczek M, Straub V, Töpf A, Palibrk A, Peric S, Rakocevic Stojanovic V, Najmabadi H, Nafissi S. Adult-onset very-long-chain acyl-CoA dehydrogenase deficiency (VLCADD). Eur J Neurol 2020; 27:2257-2266. [PMID: 32558070 DOI: 10.1111/ene.14402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/10/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND PURPOSE Very-long-chain acyl-CoA dehydrogenase deficiency (VLCADD) is a hereditary disorder of mitochondrial long-chain fatty acid oxidation that has variable presentations, including exercise intolerance, cardiomyopathy and liver disease. The aim of this study was to describe the clinical and genetic manifestations of six patients with adult-onset VLCADD. METHODS In this study, the clinical, pathological and genetic findings of six adult patients (four from Iran and two from Serbia) with VLCADD and their response to treatment are described. RESULTS The median (range) age of patients at first visit was 31 (27-38) years, and the median (range) age of onset was 26.5 (19-33) years. Parental consanguinity was present for four patients. Four patients had a history of rhabdomyolysis, and the recorded CK level ranged between 67 and 90 000 IU/l. Three patients had a history of exertional myalgia, and one patient had a non-fluctuating weakness. Through next-generation sequencing analysis, we identified six cases with variants in the ACADVL gene and a confirmed diagnosis of VLCADD. Of the total six variants identified, five were missense, and one was a novel frameshift mutation identified in two unrelated individuals. Two variants were novel, and three were previously reported. We treated the patients with a combination of L-carnitine, Coenzyme Q10 and riboflavin. Three patients responded favorably to the treatment. CONCLUSION Adult-onset VLCADD is a rare entity with various presentations. Patients may respond favorably to a cocktail of L-carnitine, Coenzyme Q10, and riboflavin.
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Affiliation(s)
- F Fatehi
- Neurology Department, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - A A Okhovat
- Neurology Department, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Y Nilipour
- Pediatric Pathology Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Mofid Children Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M Mroczek
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - V Straub
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - A Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - A Palibrk
- Neurology Clinic, Clinical Center of Serbia, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - S Peric
- Neurology Clinic, Clinical Center of Serbia, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - V Rakocevic Stojanovic
- Neurology Clinic, Clinical Center of Serbia, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - H Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - S Nafissi
- Neurology Department, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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50
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Taghizadeh S, Vazehan R, Beheshtian M, Sadeghinia F, Fattahi Z, Mohseni M, Arzhangi S, Nafissi S, Kariminejad A, Najmabadi H, Kahrizi K. Molecular Diagnosis of Hereditary Neuropathies by Whole Exome Sequencing and Expanding the Phenotype Spectrum. Arch Iran Med 2020; 23:426-433. [PMID: 32657593 DOI: 10.34172/aim.2020.39] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/08/2020] [Indexed: 11/09/2022]
Abstract
BACKGROUND Inherited peripheral neuropathies (IPNs) are a group of neuropathies affecting peripheral motor and sensory neurons. Charcot-Marie-Tooth (CMT) disease is the most common disease in this group. With recent advances in next-generation sequencing (NGS) technologies, more than 100 genes have been implicated for different types of CMT and other clinically and genetically inherited neuropathies. There are also a number of genes where neuropathy is a major feature of the disease such as spinocerebellar ataxia (SCA) and hereditary spastic paraplegia (HSP). We aimed to determine the genetic causes underlying IPNs in Iranian families. METHODS We performed whole exome sequencing (WES) for 58 PMP22 deletion-/duplication-negative unrelated Iranian patients with a spectrum of phenotypes and with a preliminary diagnosis of hereditary neuropathies. RESULTS Twenty-seven (46.6%) of the cases were genetically diagnosed with pathogenic or likely pathogenic variants. In this study, we identified genetically strong variants within genes not previously linked to any established disease phenotype in five (8.6%) patients. CONCLUSION Our results highlight the advantage of using WES for genetic diagnosis in highly heterogeneous diseases such as IPNs. Moreover, functional analysis is required for novel and uncertain variants.
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Affiliation(s)
- Sara Taghizadeh
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Student Research Committee, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Raheleh Vazehan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Farnaz Sadeghinia
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahriar Nafissi
- Department of Neurology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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