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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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Chai Y, Liu X, Bai G, Zhou N, Liu D, Zhang X, Li M, Li K, Lei H. Gut microbiome, T cell subsets, and cytokine analysis identify differential biomarkers in tuberculosis. Front Immunol 2024; 15:1323723. [PMID: 38650928 PMCID: PMC11033455 DOI: 10.3389/fimmu.2024.1323723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/21/2024] [Indexed: 04/25/2024] Open
Abstract
Introduction The gut microbiota, T cell subsets, and cytokines participate in tuberculosis (TB) pathogenesis. To date, the mechanisms by which these factors interactively promote TB development at different time points remain largely unclear. In the context of this study, We looked into the microorganisms in the digestive tract, T cell types, and cytokines related to tuberculosis. Methods According to QIIME2, we analyzed 16SrDNA sequencing of the gut microbiome on the Illumina MiSeq. Enzyme-linked immunosorbent assay was used to measure the concentrations of cytokines. Results We showed the presence of 26 identifiable differential microbiomes in the gut and 44 metabolic pathways between healthy controls and the different time points in the development of TB in patients. Five bacterial genera (Bacteroides, Bifidobacterium, Faecalibacterium, Collinsella, and Clostridium) were most closely associated with CD4/CD8, whereas three bacterial taxa (Faecalibacterium, Collinsella, and Clostridium) were most closely associated with CD4. Three bacterial taxa (Faecalibacterium, Ruminococcus, and Dorea) were most closely associated with IL-4. Ruminococcus was most closely associated with IL-2 and IL-10. Conclusion Diverse microorganisms, subsets of T cells, and cytokines, exhibiting varying relative abundances and structural compositions, were observed in both healthy controls and patients throughout distinct phases of tuberculosis. Gaining insight into the function of the gut microbiome, T cell subsets, and cytokines may help modulate therapeutic strategies for TB.
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Affiliation(s)
- Yinghui Chai
- Department of Clinical Laboratory, the 8th Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Xin Liu
- Department of Clinical Laboratory, the 8th Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Guangliang Bai
- Department of Clinical Laboratory, the 8th Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Nannan Zhou
- Department of Clinical Laboratory, the 8th Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Danfeng Liu
- Department of Clinical Laboratory, the 8th Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Xiaomeng Zhang
- First Clinical Medical College, Hebei North University, Zhangjiakou, China
| | - Min Li
- First Clinical Medical College, Hebei North University, Zhangjiakou, China
| | - Kang Li
- Department of Clinical Laboratory, the 8th Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
| | - Hong Lei
- Department of Clinical Laboratory, the 8th Medical Center of People's Liberation Army (PLA) General Hospital, Beijing, China
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Chen X, Liu J, Wei QQ, Ou RW, Cao B, Yuan X, Hou Y, Zhang L, Shang H. Chinese families with autosomal recessive hereditary spastic paraplegia caused by mutations in SPG11. BMC Neurol 2020; 20:2. [PMID: 31900114 PMCID: PMC6941247 DOI: 10.1186/s12883-019-1593-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/29/2019] [Indexed: 02/08/2023] Open
Abstract
Background Spastic paraplegia type 11 (SPG11) mutations are the most frequent cause of autosomal recessive hereditary spastic paraplegia (ARHSP). We are aiming to identify the causative mutations in SPG11 among families referred to our center with ARHSP in a Chinese population. Methods Targeted next-generation sequencing was performed on the patients to identify disease-causing mutations. Variants were analyzed according to their predicted pathogenicity and their relevance to the clinical phenotypes. The segregation in the family members was validated by Sanger sequencing. Results A total of 12 mutations in SPG11 gene from 9 index cases were identified, including 6 frameshift mutations, 3 missense mutations, 1 nonsense mutation, 1 splicing mutation, and 1 intron deletion mutation. In 6 of these patients, the mutations were homozygous, and the other 3 patients carried two compound heterozygous mutations. Six mutations were novel; 2 were classified as pathogenic, 1 were considered as likely pathogenic, and the other 3 were variants of unknown significance. Additionally, 1 missense heterozygous variant we found was also carried by amyotrophic lateral sclerosis (ALS) patient. Clinically and electrophysiologically, some of our ARHSP patients partially shared various features of autosomal-recessive juvenile amyotrophic lateral sclerosis (ARJALS), including combination of both UMN and LMN degeneration. Conclusions The results contribute to extending of the SPG11 gene mutation spectrum and emphasizing a putative link between ARHSP and ARJALS.
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Affiliation(s)
- Xueping Chen
- Department of Neurology, West China Hospital, Sichuan University, No. 37 Guoxue Xiang, Chengdu, 610041, Sichuan, China
| | - Jiao Liu
- Department of Neurology, West China Hospital, Sichuan University, No. 37 Guoxue Xiang, Chengdu, 610041, Sichuan, China
| | - Qian-Qian Wei
- Department of Neurology, West China Hospital, Sichuan University, No. 37 Guoxue Xiang, Chengdu, 610041, Sichuan, China
| | - Ru Wei Ou
- Department of Neurology, West China Hospital, Sichuan University, No. 37 Guoxue Xiang, Chengdu, 610041, Sichuan, China
| | - Bei Cao
- Department of Neurology, West China Hospital, Sichuan University, No. 37 Guoxue Xiang, Chengdu, 610041, Sichuan, China
| | - Xiaoqin Yuan
- Department of Neurology, West China Hospital, Sichuan University, No. 37 Guoxue Xiang, Chengdu, 610041, Sichuan, China
| | - Yanbing Hou
- Department of Neurology, West China Hospital, Sichuan University, No. 37 Guoxue Xiang, Chengdu, 610041, Sichuan, China
| | - Lingyu Zhang
- Department of Neurology, West China Hospital, Sichuan University, No. 37 Guoxue Xiang, Chengdu, 610041, Sichuan, China
| | - Huifang Shang
- Department of Neurology, West China Hospital, Sichuan University, No. 37 Guoxue Xiang, Chengdu, 610041, Sichuan, China.
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Mackley MP, Capps B. Expect the unexpected: screening for secondary findings in clinical genomics research. Br Med Bull 2017; 122:109-122. [PMID: 28398474 DOI: 10.1093/bmb/ldx009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/10/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Due to decreasing cost, and increasing speed and precision, genomic sequencing in research is resulting in the generation of vast amounts of genetic data. The question of how to manage that information has been an area of significant debate. In particular, there has been much discussion around the issue of 'secondary findings' (SF)-findings unrelated to the research that have diagnostic significance. SOURCES OF DATA The following includes ethical commentaries, guidelines and policies in respect to large-scale clinical genomics studies. AREAS OF AGREEMENT Research participant autonomy and their informed consent are paramount-policies around SF must be made clear and participants must have the choice as to which results they wish to receive, if any. AREAS OF CONTROVERSY While many agree that clinically 'actionable' findings should be returned, some question whether they should be actively sought within a research protocol. GROWING POINTS SF present challenges to a growing field; diverse policies around their management have the potential to hinder collaboration and future research. AREAS TIMELY FOR DEVELOPING RESEARCH The impact of returning SF and accurate estimates of their clinical utility are needed to inform future protocol design.
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Affiliation(s)
- Michael P Mackley
- Radcliffe Department of Medicine, University of Oxford, Level 6 West Wing, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Benjamin Capps
- Department of Bioethics, Faculty of Medicine, Dalhousie University, 5849 University Avenue, Room C-312, CRC Bldg, PO Box 15000, Halifax NS, Canada B3H 4R2
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Abstract
PURPOSE OF REVIEW Neuromuscular diseases are clinically and genetically heterogeneous and probably contain the greatest proportion of causative Mendelian defects than any other group of conditions. These disorders affect muscle and/or nerves with neonatal, childhood or adulthood onset, with significant disability and early mortality. Along with heterogeneity, unidentified and often very large genes require complementary and comprehensive methods in routine molecular diagnosis. Inevitably, this leads to increased diagnostic delays and challenges in the interpretation of genetic variants. RECENT FINDINGS The application of next-generation sequencing, as a research and diagnostic strategy, has made significant progress into solving many of these problems. The analysis of these data is by no means simple, and the clinical input is essential to interpret results. SUMMARY In this review, we describe using examples the recent advances in the genetic diagnosis of neuromuscular disorders, in research and clinical practice and the latest developments that are underway in next-generation sequencing. We also discuss the latest collaborative initiatives such as the Genomics England (Department of Health, UK) genome sequencing project that combine rare disease clinical phenotyping with genomics, with the aim of defining the vast majority of rare disease genes in patients as well as modifying risks and pharmacogenomics factors.
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