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Shafique A, Nadeem A, Aslam F, Manzoor H, Noman M, Wohler E, Witmer PD, Sobreira N, Naz S. Identification and analyses of exonic and copy number variants in spastic paraplegia. Sci Rep 2024; 14:14331. [PMID: 38906889 PMCID: PMC11192879 DOI: 10.1038/s41598-024-64922-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/14/2024] [Indexed: 06/23/2024] Open
Abstract
Hereditary spastic paraplegias are a diverse group of degenerative disorders that are clinically categorized as isolated; with involvement of lower limb spasticity, or symptomatic, where spastic paraplegia is complicated by further neurological features. We sought to identify the underlying genetic causes of these disorders in the participating patients. Three consanguineous families with multiple affected members were identified by visiting special schools in the Punjab Province. DNA was extracted from blood samples of the participants. Exome sequencing was performed for selected patients from the three families, and the data were filtered to identify rare homozygous variants. ExomeDepth was used for the delineation of the copy number variants. All patients had varying degrees of intellectual disabilities, poor speech development, spasticity, a wide-based gait or an inability to walk and hypertonia. In family RDHR07, a homozygous deletion involving multiple exons and introns of SPG11 (NC000015.9:g.44894055_449028del) was found and correlated with the phenotype of the patients who had spasticity and other complex movement disorders, but not those who exhibited ataxic or indeterminate symptoms as well. In families ANMD03 and RDFA06, a nonsense variant, c.985C > T;(p.Arg329Ter) in DDHD2 and a frameshift insertion‒deletion variant of AP4B1, c.965-967delACTinsC;p.(Tyr322SerfsTer14), were identified which were homozygous in the patients while the obligate carriers in the respective pedigrees were heterozygous. All variants were ultra-rare with none, or very few carriers identified in the public databases. The three loss of function variants are likely to cause nonsense-mediated decay of the respective transcripts. Our research adds to the genetic variability associated with the SPG11 and AP4B1 variants and emphasizes the genetic heterogeneity of hereditary spastic paraplegia.
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Affiliation(s)
- Anum Shafique
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Ayesha Nadeem
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Faiza Aslam
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Humera Manzoor
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
| | - Muhammad Noman
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan
- Department of Biochemistry, Faisalabad Medical University, Faisalabad, Pakistan
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Baylor Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | - P Dane Witmer
- McKusick-Nathans Department of Genetic Medicine, Baylor Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Baylor Hopkins Center for Mendelian Genomics, Baltimore, MD, USA
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Pakistan.
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Orsini A, Santangelo A, Carmignani A, Camporeale A, Massart F, Tyutyusheva N, Peroni DG, Foiadelli T, Ferretti A, Toschi B, Romano S, Bonuccelli A. An Ultra-Rare Mixed Phenotype with Combined AP-4 and ERF Mutations: The First Report in a Pediatric Patient and a Literature Review. Genes (Basel) 2024; 15:436. [PMID: 38674371 PMCID: PMC11049481 DOI: 10.3390/genes15040436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The adaptor protein 4 (AP-4) constitutes a conserved hetero-tetrameric complex within the family of adaptor protein (AP) complex, crucial for the signal-mediated trafficking of integral membrane proteins. Mutations affecting all subunits of the AP-4 complex have been linked to autosomal-recessive cerebral palsy and a complex hereditary spastic paraparesis (HSP) phenotype. Our report details the case of a 14-year-old boy born to consanguineous parents, presenting psychomotor delay, severe intellectual disability, microcephaly, and trigonocephaly. Despite a history of febrile seizures, subsequent years were devoid of seizures, with normal EEG. Exome sequencing revealed pathogenic variants in both the AP4B1 and ERF genes. Significantly, the patient exhibited features associated with AP4B1 mutations, including distinctive traits such as cranial malformations. The ERF gene variant, linked to craniosynostosis, likely contributes to the observed trigonocephaly. This case represents the initial documentation of a concurrent mutation in the AP4B1 and ERF genes, underscoring the critical role of exome analysis in unraveling complex phenotypes. Understanding these complex genotypes offers valuable insights into broader syndromic conditions, facilitating comprehensive patient management.
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Affiliation(s)
- Alessandro Orsini
- Pediatric Neurology, Pediatric Department, AOUP Santa Chiara Hospital, 56100 Pisa, Italy; (A.O.); (A.B.)
| | - Andrea Santangelo
- Pediatric Neurology, Pediatric Department, AOUP Santa Chiara Hospital, 56100 Pisa, Italy; (A.O.); (A.B.)
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, 16126 Genoa, Italy
| | - Alessandra Carmignani
- Pediatric Department, AOUP Santa Chiara Hospital, 56100 Pisa, Italy; (A.C.); (A.C.); (D.G.P.)
| | - Anna Camporeale
- Pediatric Department, AOUP Santa Chiara Hospital, 56100 Pisa, Italy; (A.C.); (A.C.); (D.G.P.)
| | - Francesco Massart
- Pediatric Endocrinology, Pediatric Department, AOUP Santa Chiara Hospital, 56100 Pisa, Italy; (F.M.); (N.T.)
| | - Nina Tyutyusheva
- Pediatric Endocrinology, Pediatric Department, AOUP Santa Chiara Hospital, 56100 Pisa, Italy; (F.M.); (N.T.)
| | - Diego Giampietro Peroni
- Pediatric Department, AOUP Santa Chiara Hospital, 56100 Pisa, Italy; (A.C.); (A.C.); (D.G.P.)
| | - Thomas Foiadelli
- Clinica Pediatrica, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy;
| | - Alessandro Ferretti
- Pediatrics Unit, Neuroscience, Mental Health and Sense Organs (NESMOS) Department, Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy;
| | - Benedetta Toschi
- Division of Medical Genetics, Department of Medical and Oncological Area, University-Hospital, 56126 Pisa, Italy; (B.T.); (S.R.)
| | - Silvia Romano
- Division of Medical Genetics, Department of Medical and Oncological Area, University-Hospital, 56126 Pisa, Italy; (B.T.); (S.R.)
| | - Alice Bonuccelli
- Pediatric Neurology, Pediatric Department, AOUP Santa Chiara Hospital, 56100 Pisa, Italy; (A.O.); (A.B.)
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Salayev K, Rocca C, Kaiyrzhanov R, Guliyeva U, Guliyeva S, Mursalova A, Rahman F, Anwar N, Zafar F, Jan F, Rana N, Maqbool S, Efthymiou S, Houlden H. AP4B1-associated hereditary spastic paraplegia: Expansion of clinico-genetic phenotype and geographic range. Eur J Med Genet 2022; 65:104620. [PMID: 36122674 DOI: 10.1016/j.ejmg.2022.104620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/22/2022] [Accepted: 09/12/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND Hereditary spastic paraplegias (HSP) are a group of neurodegenerative diseases that present with weakness and stiffness in the lower limb muscles and lead to progressive neurological decline. Bi-allelic loss-of-function variants in genes that encode subunits of the adaptor protein complex 4 (AP-4) lead to complex HSP. This study aimed to identify causative genetic variants in consanguineous families with HSP from Azerbaijan and Pakistan. METHODS We performed a thorough clinical and neuroradiological characterization followed by exome sequencing in 7 patients from 3 unrelated families. Segregation analysis was subsequently performed by Sanger sequencing. RESULTS We describe 7 patients (4 males, 2-31 years of age) with developmental delay and spasticity. Similar to the previously reported cases with AP4B1-associated HSP, cases in the present report besides spasticity in the lower limbs had additional features including microcephaly, facial dysmorphism, infantile hypotonia, and epilepsy. The imaging findings included thin corpus callosum, white matter loss, and ventriculomegaly. CONCLUSION In this study, we report 7 novel cases of HSP caused by bi-allelic variants in AP4B1 in Azerbaijani and Pakistani families. Our observations will help clinicians observe and compare common and unique clinical features of AP4B1-associated HSP patients, further improving our current understanding of HSP.
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Affiliation(s)
- Kamran Salayev
- Azerbaijan Medical University, Department of Neurology, Baku, AZ, 1010, Azerbaijan
| | - Clarissa Rocca
- University College London, Institute of Neurology, Department of Neuromuscular Disorders, Queen Square, WC1N 3BG, London, UK
| | - Rauan Kaiyrzhanov
- University College London, Institute of Neurology, Department of Neuromuscular Disorders, Queen Square, WC1N 3BG, London, UK
| | - Ulviyya Guliyeva
- MediClub Hospital, 45, Uzeyir Hajibeyli Str., Baku, AZ, 1010, Azerbaijan
| | - Sughra Guliyeva
- MediClub Hospital, 45, Uzeyir Hajibeyli Str., Baku, AZ, 1010, Azerbaijan
| | - Aytan Mursalova
- Baku City Gerontologic Centre, Azadliq Ave., Baku, Azerbaijan
| | - Fatima Rahman
- Development and Behavioral Pediatrics Department, Institute of Child Health and the Children Hospital, Lahore, 54000, Pakistan
| | - Najwa Anwar
- Development and Behavioral Pediatrics Department, Institute of Child Health and the Children Hospital, Lahore, 54000, Pakistan
| | - Faisal Zafar
- Department of Paediatric Neurology, Children's Hospital and Institute of Child Health, Multan, Pakistan
| | - Farida Jan
- Department of Paediatrics and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Nuzhat Rana
- Department of Paediatric Neurology, Children's Hospital and Institute of Child Health, Multan, Pakistan
| | - Shazia Maqbool
- Development and Behavioral Pediatrics Department, Institute of Child Health and the Children Hospital, Lahore, 54000, Pakistan
| | - Stephanie Efthymiou
- University College London, Institute of Neurology, Department of Neuromuscular Disorders, Queen Square, WC1N 3BG, London, UK
| | - Henry Houlden
- University College London, Institute of Neurology, Department of Neuromuscular Disorders, Queen Square, WC1N 3BG, London, UK.
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Recent development in emerging phosphorene based novel materials: Progress, challenges, prospects and their fascinating sensing applications. PROG SOLID STATE CH 2021. [DOI: 10.1016/j.progsolidstchem.2021.100336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Rudenskaya GE, Guseva DM, Mironovich OL, Kadnikova VA, Dadali EL, Komar'kov IF, Novoselova OG, Ryzhkova OP. [AP4-assocated hereditary spastic paraplegias]. Zh Nevrol Psikhiatr Im S S Korsakova 2021; 121:71-78. [PMID: 33728854 DOI: 10.17116/jnevro202112102171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
OBJECTIVE In the course of studies of spastic paraplegias in Russian patients to detect AP4-associated forms, estimate their proportion in the total SPG group and analyze clinical and molecular characteristics. MATERIAL AND METHODS Five families of Russian ethnicity: four with SPG47, one with SPG51 (4 girls and a boy aged 2.5-9 years) were studied. Clinical and genealogical methods, whole-exome sequencing (WES) and verification by familial Sanger sequencing were used. RESULTS In our total group, including 118 families with 21 different forms, SPG AP4-associated forms accounted for 4.2% owing mainly to SPG47 (3.4%, 5th place in SPG structure; 20% and 2nd place in AE subgroup.) In non-consanguineous, unrelated SPG47 families three patients had identical genotypes: homozygosity for an earlier reported mutation c.1160_1161 delCA (p.Thr387ArgfsTer30) in AP4B1 exon 6; the 4th patient was compound-heterozygous for the same mutation and novel c.1240C>T (p.Gln414Ter) in exon 7. Frequency of c.1160_1161 delCA may be caused by founder effect in Slavic populations though the idea needs additional studies. The SPG51 patient was compound heterozygous for novel AP4E1 mutations c.2604delA (p.Ser868fs) and c.3346A>G (p.Arg1116Gly). Parent's heterozygosity in all cases was confirmed by Sanger sequencing. Phenotypes were typical: early development delay, muscle hypotony transforming into sever spasticity, mental deficiency, microceplaly (in all SPG47 cases), epilepsy (in 3 SPG47 and SPG51 cases), MRI changes, mainly hydrocephalus and/or hypoplasia of corpus callosum (in 3 SPG47 cases) and few extraneural signs. CONCLUSION AP4-associated SPG should be taken into consideration in patients with early-onset severe nervous diseases mimicking non-genetic organic CNS disorders and massive exome sequencing (WES or other variants) should be performed.
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Affiliation(s)
| | - D M Guseva
- Research Centre for Medical Genetics, Moscow, Russia
| | | | - V A Kadnikova
- Research Centre for Medical Genetics, Moscow, Russia
| | - E L Dadali
- Research Centre for Medical Genetics, Moscow, Russia
| | | | | | - O P Ryzhkova
- Research Centre for Medical Genetics, Moscow, Russia
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Whole exome sequencing uncovered highly penetrant recessive mutations for a spectrum of rare genetic pediatric diseases in Bangladesh. NPJ Genom Med 2021; 6:14. [PMID: 33594065 PMCID: PMC7887195 DOI: 10.1038/s41525-021-00173-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/06/2021] [Indexed: 01/31/2023] Open
Abstract
Collectively, rare genetic diseases affect a significant number of individuals worldwide. In this study, we have conducted whole-exome sequencing (WES) and identified underlying pathogenic or likely pathogenic variants in five children with rare genetic diseases. We present evidence for disease-causing autosomal recessive variants in a range of disease-associated genes such as DHH-associated 46,XY gonadal dysgenesis (GD) or 46,XY sex reversal 7, GNPTAB-associated mucolipidosis II alpha/beta (ML II), BBS1-associated Bardet-Biedl Syndrome (BBS), SURF1-associated Leigh Syndrome (LS) and AP4B1-associated spastic paraplegia-47 (SPG47) in unrelated affected members from Bangladesh. Our analysis pipeline detected three homozygous mutations, including a novel c. 863 G > C (p.Pro288Arg) variant in DHH, and two compound heterozygous variants, including two novel variants: c.2972dupT (p.Met991Ilefs*) in GNPTAB and c.229 G > C (p.Gly77Arg) in SURF1. All mutations were validated by Sanger sequencing. Collectively, this study adds to the genetic heterogeneity of rare genetic diseases and is the first report elucidating the genetic profile of (consanguineous and nonconsanguineous) rare genetic diseases in the Bangladesh population.
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The role of AP-4 in cargo export from the trans-Golgi network and hereditary spastic paraplegia. Biochem Soc Trans 2020; 48:1877-1888. [PMID: 33084855 DOI: 10.1042/bst20190664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/22/2020] [Accepted: 09/29/2020] [Indexed: 01/02/2023]
Abstract
Heterotetrameric adaptor protein (AP) complexes play key roles in protein sorting and transport vesicle formation in the endomembrane system of eukaryotic cells. One of these complexes, AP-4, was identified over 20 years ago but, up until recently, its function remained unclear. AP-4 associates with the trans-Golgi network (TGN) through interaction with small GTPases of the ARF family and recognizes transmembrane proteins (i.e. cargos) having specific sorting signals in their cytosolic domains. Recent studies identified accessory proteins (tepsin, RUSC2 and the FHF complex) that co-operate with AP-4, and cargos (amyloid precursor protein, ATG9A and SERINC3/5) that are exported from the TGN in an AP-4-dependent manner. Defective export of ATG9A from the TGN in AP-4-deficient cells was shown to reduce ATG9A delivery to pre-autophagosomal structures, impairing autophagosome formation and/or maturation. In addition, mutations in AP-4-subunit genes were found to cause neurological dysfunction in mice and a form of complicated hereditary spastic paraplegia referred to as 'AP-4-deficiency syndrome' in humans. These findings demonstrated that mammalian AP-4 is required for the development and function of the central nervous system, possibly through its role in the sorting of ATG9A for the maintenance of autophagic homeostasis. In this article, we review the properties and functions of AP-4, and discuss how they might explain the clinical features of AP-4 deficiency.
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