1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Awuah WA, Tan JK, Shkodina AD, Ferreira T, Adebusoye FT, Mazzoleni A, Wellington J, David L, Chilcott E, Huang H, Abdul-Rahman T, Shet V, Atallah O, Kalmanovich J, Jiffry R, Madhu DE, Sikora K, Kmyta O, Delva MY. Hereditary spastic paraplegia: Novel insights into the pathogenesis and management. SAGE Open Med 2023; 12:20503121231221941. [PMID: 38162912 PMCID: PMC10757446 DOI: 10.1177/20503121231221941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Hereditary spastic paraplegia is a genetically heterogeneous neurodegenerative disorder characterised primarily by muscle stiffness in the lower limbs. Neurodegenerative disorders are conditions that result from cellular and metabolic abnormalities, many of which have strong genetic ties. While ageing is a known contributor to these changes, certain neurodegenerative disorders can manifest early in life, progressively affecting a person's quality of life. Hereditary spastic paraplegia is one such condition that can appear in individuals of any age. In hereditary spastic paraplegia, a distinctive feature is the degeneration of long nerve fibres in the corticospinal tract of the lower limbs. This degeneration is linked to various cellular and metabolic processes, including mitochondrial dysfunction, remodelling of the endoplasmic reticulum membrane, autophagy, abnormal myelination processes and alterations in lipid metabolism. Additionally, hereditary spastic paraplegia affects processes like endosome membrane trafficking, oxidative stress and mitochondrial DNA polymorphisms. Disease-causing genetic loci and associated genes influence the progression and severity of hereditary spastic paraplegia, potentially affecting various cellular and metabolic functions. Although hereditary spastic paraplegia does not reduce a person's lifespan, it significantly impairs their quality of life as they age, particularly with more severe symptoms. Regrettably, there are currently no treatments available to halt or reverse the pathological progression of hereditary spastic paraplegia. This review aims to explore the metabolic mechanisms underlying the pathophysiology of hereditary spastic paraplegia, emphasising the interactions of various genes identified in recent network studies. By comprehending these associations, targeted molecular therapies that address these biochemical processes can be developed to enhance treatment strategies for hereditary spastic paraplegia and guide clinical practice effectively.
Collapse
Affiliation(s)
| | | | - Anastasiia D Shkodina
- Department of Neurological Diseases, Poltava State Medical University, Poltava, Ukraine
| | - Tomas Ferreira
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Adele Mazzoleni
- Barts and the London School of Medicine and Dentistry, London, UK
| | - Jack Wellington
- Cardiff University School of Medicine, Cardiff University, Wales, UK
| | - Lian David
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Ellie Chilcott
- Cardiff University School of Medicine, Cardiff University, Wales, UK
| | - Helen Huang
- Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | | | - Vallabh Shet
- Faculty of Medicine, Bangalore Medical College and Research Institute, Karnataka, India
| | - Oday Atallah
- Department of Neurosurgery, Hannover Medical School, Hannover, Germany
| | | | - Riaz Jiffry
- Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Dublin, Ireland
| | | | | | | | - Mykhailo Yu Delva
- Department of Neurological Diseases, Poltava State Medical University, Poltava, Ukraine
| |
Collapse
|
3
|
Martins S, Yahia A, Costa IPD, Siddig HE, Abubaker R, Koko M, Corral-Juan M, Matilla-Dueñas A, Brice A, Durr A, Leguern E, Ranum LPW, Amorim A, Elsayed LEO, Stevanin G, Sequeiros J. Machado-Joseph disease in a Sudanese family links East Africa to Portuguese families and allows reestimation of ancestral age of the Machado lineage. Hum Genet 2023; 142:1747-1754. [PMID: 37957369 PMCID: PMC10676304 DOI: 10.1007/s00439-023-02611-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
Machado-Joseph disease (MJD/SCA3) is the most frequent dominant ataxia worldwide. It is caused by a (CAG)n expansion. MJD has two major ancestral backgrounds: the Machado lineage, found mainly in Portuguese families; and the Joseph lineage, present in all five continents, probably originating in Asia. MJD has been described in a few African and African-American families, but here we report the first diagnosed in Sudan to our knowledge. The proband presented with gait ataxia at age 24; followed by muscle cramps and spasticity, and dysarthria, by age 26; he was wheel-chair bound at 29 years of age. His brother had gait problems from age 20 years and, by age 21, lost the ability to run, showed dysarthria and muscle cramps. To assess the mutational origin of this family, we genotyped 30 SNPs and 7 STRs flanking the ATXN3_CAG repeat in three siblings and the non-transmitting father. We compared the MJD haplotype segregating in the family with our cohort of MJD families from diverse populations. Unlike all other known families of African origin, the Machado lineage was observed in Sudan, being shared with 86 Portuguese, 2 Spanish and 2 North-American families. The STR-based haplotype of Sudanese patients, however, was distinct, being four steps (2 STR mutations and 2 recombinations) away from the founder haplotype shared by 47 families, all of Portuguese extraction. Based on the phylogenetic network constructed with all MJD families of the Machado lineage, we estimated a common ancestry at 3211 ± 693 years ago.
Collapse
Affiliation(s)
- Sandra Martins
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Ashraf Yahia
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
- Sorbonne University, Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Paris, France
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institutet and Stockholm Health Care Services, Stockholm, Sweden
| | - Inês P D Costa
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Hassab E Siddig
- Division of Neurology, Sudan Medical Council, Khartoum, Sudan
| | - Rayan Abubaker
- Sudanese Neurogenetics Research Group, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Mahmoud Koko
- Sudanese Neurogenetics Research Group, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Marc Corral-Juan
- Functional and Translational Neurogenetics Unit, Department of Neuroscience, Health Sciences Research Institute Germans Trias I Pujol (IGTP)-Universitat Autònoma de Barcelona, Can Ruti Campus, Badalona, Barcelona, Spain
| | - Antoni Matilla-Dueñas
- Functional and Translational Neurogenetics Unit, Department of Neuroscience, Health Sciences Research Institute Germans Trias I Pujol (IGTP)-Universitat Autònoma de Barcelona, Can Ruti Campus, Badalona, Barcelona, Spain
| | - Alexis Brice
- Sorbonne University, Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Paris, France
| | - Alexandra Durr
- Sorbonne University, Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Paris, France
| | - Eric Leguern
- Sorbonne University, Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Paris, France
- Genetics Department, APHP, Pitié-Salpêtrière Hospital, Paris, France
| | - Laura P W Ranum
- Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, FL, USA
| | - António Amorim
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IPATIMUP-Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Liena E O Elsayed
- Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Giovanni Stevanin
- Sorbonne University, Paris Brain Institute - ICM, Inserm, CNRS, AP-HP, Paris, France
- Univ. Bordeaux, CNRS-Centre National de la Recherche Scientifique, INCIA-Institut de Neurosciences Cognitives et Intégratives d'Aquitaine, UMR 5287, Bordeaux, France
- EPHE-École Pratique des Hautes Études, CNRS-Centre National de la Recherche Scientifique, INCIA-Institut de Neurosciences Cognitives et Intégratives d'Aquitaine, UMR 5287, Paris, France
| | - Jorge Sequeiros
- i3S-Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.
- UnIGENe and CGPP-Centro de Genética Preditiva e Preventiva, IBMC-Institute for Molecular and Cell Biology, University of Porto, Porto, Portugal.
- ICBAS School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal.
| |
Collapse
|