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Cadoni MPL, Coradduzza D, Congiargiu A, Sedda S, Zinellu A, Medici S, Nivoli AM, Carru C. Platelet Dynamics in Neurodegenerative Disorders: Investigating the Role of Platelets in Neurological Pathology. J Clin Med 2024; 13:2102. [PMID: 38610867 PMCID: PMC11012481 DOI: 10.3390/jcm13072102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Background: Neurological disorders, particularly those associated with aging, pose significant challenges in early diagnosis and treatment. The identification of specific biomarkers, such as platelets (PLTs), has emerged as a promising strategy for early detection and intervention in neurological health. This systematic review aims to explore the intricate relationship between PLT dynamics and neurological health, focusing on their potential role in cognitive functions and the pathogenesis of cognitive disorders. Methods: Adhering to PRISMA guidelines, a comprehensive search strategy was employed in the PubMed and Scholar databases to identify studies on the role of PLTs in neurological disorders published from 2013 to 2023. The search criteria included studies focusing on PLTs as biomarkers in neurological disorders, their dynamics, and their potential in monitoring disease progression and therapy effectiveness. Results: The systematic review included 104 studies, revealing PLTs as crucial biomarkers in neurocognitive disorders, acting as inflammatory mediators. The findings suggest that PLTs share common features with altered neurons, which could be utilised for monitoring disease progression and evaluating the effectiveness of treatments. PLTs are identified as significant biomarkers for detecting neurological disorders in their early stages and understanding the pathological events leading to neuronal death. Conclusions: The systematic review underscores the critical role of PLTs in neurological disorders, highlighting their potential as biomarkers for the early detection and monitoring of disease progression. However, it also emphasises the need for further research to solidify the use of PLTs in neurological disorders, aiming to enhance early diagnosis and intervention strategies.
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Affiliation(s)
| | | | | | - Stefania Sedda
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Angelo Zinellu
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Serenella Medici
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Alessandra Matilde Nivoli
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy
- Psychiatric Unit Clinic of the University Hospital, 07100 Sassari, Italy
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
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Mahmoud M, Harting J, Corbitt H, Chen X, Jhangiani SN, Doddapaneni H, Meng Q, Han T, Lambert C, Zhang S, Baybayan P, Henno G, Shen H, Hu J, Han Y, Riegler C, Metcalf G, Henno G, Chinn IK, Eberle MA, Kingan S, Farinholt T, Carvalho CM, Gibbs RA, Kronenberg Z, Muzny D, Sedlazeck FJ. Closing the gap: Solving complex medically relevant genes at scale. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.14.24304179. [PMID: 38562723 PMCID: PMC10984040 DOI: 10.1101/2024.03.14.24304179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Comprehending the mechanism behind human diseases with an established heritable component represents the forefront of personalized medicine. Nevertheless, numerous medically important genes are inaccurately represented in short-read sequencing data analysis due to their complexity and repetitiveness or the so-called 'dark regions' of the human genome. The advent of PacBio as a long-read platform has provided new insights, yet HiFi whole-genome sequencing (WGS) cost remains frequently prohibitive. We introduce a targeted sequencing and analysis framework, Twist Alliance Dark Genes Panel (TADGP), designed to offer phased variants across 389 medically important yet complex autosomal genes. We highlight TADGP accuracy across eleven control samples and compare it to WGS. This demonstrates that TADGP achieves variant calling accuracy comparable to HiFi-WGS data, but at a fraction of the cost. Thus, enabling scalability and broad applicability for studying rare diseases or complementing previously sequenced samples to gain insights into these complex genes. TADGP revealed several candidate variants across all cases and provided insight into LPA diversity when tested on samples from rare disease and cardiovascular disease cohorts. In both cohorts, we identified novel variants affecting individual disease-associated genes (e.g., IKZF1, KCNE1). Nevertheless, the annotation of the variants across these 389 medically important genes remains challenging due to their underrepresentation in ClinVar and gnomAD. Consequently, we also offer an annotation resource to enhance the evaluation and prioritization of these variants. Overall, we can demonstrate that TADGP offers a cost-efficient and scalable approach to routinely assess the dark regions of the human genome with clinical relevance.
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Affiliation(s)
- Medhat Mahmoud
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - John Harting
- Pacific Biosciences, Menlo Park, California, USA
| | | | - Xiao Chen
- Pacific Biosciences, Menlo Park, California, USA
| | | | - Harsha Doddapaneni
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Qingchang Meng
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Tina Han
- Twist Bioscience, South San Francisco, USA
| | | | - Siyuan Zhang
- Pacific Biosciences, Menlo Park, California, USA
| | | | - Geoff Henno
- Pacific Biosciences, Menlo Park, California, USA
| | - Hua Shen
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Jianhong Hu
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Yi Han
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | | | - Ginger Metcalf
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Geoff Henno
- Pacific Biosciences, Menlo Park, California, USA
| | - Ivan K. Chinn
- Department of Pediatrics, Section of Immunology Allergy and Rheumatology, Center for Human Immunobiology, Texas Children’s Hospital and Baylor College of Medicine, Houston, Texas, USA
| | | | - Sarah Kingan
- Pacific Biosciences, Menlo Park, California, USA
| | | | | | - Richard A. Gibbs
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | | | - Donna Muzny
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
| | - Fritz J. Sedlazeck
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Computer Science, Rice University, Houston, Texas, USA
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Khowal S, Zhang D, Yong WH, Heaney AP. Whole-exome sequencing reveals genetic variants that may play a role in neurocytomas. J Neurooncol 2024; 166:471-483. [PMID: 38319496 DOI: 10.1007/s11060-024-04567-9] [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: 12/16/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024]
Abstract
OBJECTIVES Neurocytomas (NCs) are rare intracranial tumors that can often be surgically resected. However, disease course is unpredictable in many patients and medical therapies are lacking. We have used whole exome sequencing to explore the molecular etiology for neurocytoma and assist in target identification to develop novel therapeutic interventions. METHODS We used whole exome sequencing (WES) to compare the molecular landscape of 21 primary & recurrent NCs to five normal cerebellar control samples. WES data was analyzed using the Qiagen Clinical Insight program, variants of interest (VOI) were interrogated using ConSurf, ScoreCons, & Ingenuity Pathway Analysis Software to predict their potential functional effects, and Copy number variations (CNVs) in the genes of interest were analyzed by Genewiz (Azenta Life Sciences). RESULTS Of 40 VOI involving thirty-six genes, 7 were pathogenic, 17 likely-pathogenic, and 16 of uncertain-significance. Of seven pathogenic NC associated variants, Glucosylceramidase beta 1 [GBA1 c.703T > C (p.S235P)] was mutated in 5/21 (24%), Coagulation factor VIII [F8 c.3637dupA (p.I1213fs*28)] in 4/21 (19%), Phenylalanine hydroxylase [PAH c.975C > A (p.Y325*)] in 3/21 (14%), and Fanconi anemia complementation group C [FANCC c.1162G > T (p.G388*)], Chromodomain helicase DNA binding protein 7 [CHD7 c.2839C > T (p.R947*)], Myosin VIIA [MYO7A c.940G > T (p.E314*)] and Dynein axonemal heavy chain 11 [DNAH11 c.3544C > T (p.R1182*)] in 2/21 (9.5%) NCs respectively. CNVs were noted in 85% of these latter 7 genes. Interestingly, a Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2 [CTDSP2 c.472G > A (p.E158K)] of uncertain significance was also found in > 70% of NC cases. INTERPRETATION The variants of interest we identified in the NCs regulate a variety of neurological processes including cilia motility, cell metabolism, immune responses, and DNA damage repair and provide novel insights into the molecular pathogenesis of these extremely rare tumors.
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Affiliation(s)
- Sapna Khowal
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Dongyun Zhang
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - William H Yong
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, 92868, USA
| | - Anthony P Heaney
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
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Chandrababu K, Radhakrishnan V, Anjana AS, Rajan R, Sivan U, Krishnan S, Baby Chakrapani PS. Unravelling the Parkinson's puzzle, from medications and surgery to stem cells and genes: a comprehensive review of current and future management strategies. Exp Brain Res 2024; 242:1-23. [PMID: 38015243 DOI: 10.1007/s00221-023-06735-1] [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: 06/19/2023] [Accepted: 10/29/2023] [Indexed: 11/29/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder, prevalent in the elderly population. Neuropathological hallmarks of PD include loss of dopaminergic cells in the nigro-striatal pathway and deposition of alpha-synuclein protein in the neurons and synaptic terminals, which lead to a complex presentation of motor and non-motor symptoms. This review focuses on various aspects of PD, from clinical diagnosis to currently accepted treatment options, such as pharmacological management through dopamine replacement and surgical techniques such as deep brain stimulation (DBS). The review discusses in detail the potential of emerging stem cell-based therapies and gene therapies to be adopted as a cure, in contrast to the present symptomatic treatment in PD. The potential sources of stem cells for autologous and allogeneic stem cell therapy have been discussed, along with the progress evaluation of pre-clinical and clinical trials. Even though recent techniques hold great potential to improve the lives of PD patients, we present the importance of addressing the safety, efficacy, ethical, cost, and regulatory concerns before scaling them to clinical use.
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Affiliation(s)
- Krishnapriya Chandrababu
- Centre for Neuroscience, Department of Biotechnology, Cochin University for Science and Technology, Kochi, Kerala, 682 022, India
| | - Vineeth Radhakrishnan
- Comprehensive Care Centre for Movement Disorders, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, India
| | - A S Anjana
- Centre for Neuroscience, Department of Biotechnology, Cochin University for Science and Technology, Kochi, Kerala, 682 022, India
| | - Rahul Rajan
- Centre for Neuroscience, Department of Biotechnology, Cochin University for Science and Technology, Kochi, Kerala, 682 022, India
| | - Unnikrishnan Sivan
- Faculty of Fisheries Engineering, Kerala University of Fisheries and Ocean Studies, Kochi, Kerala, India
| | - Syam Krishnan
- Comprehensive Care Centre for Movement Disorders, Department of Neurology, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala, India
| | - P S Baby Chakrapani
- Centre for Neuroscience, Department of Biotechnology, Cochin University for Science and Technology, Kochi, Kerala, 682 022, India.
- Centre for Excellence in Neurodegeneration and Brain Health (CENBH), Kochi, Kerala, India.
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GBA1 Gene Mutations in α-Synucleinopathies-Molecular Mechanisms Underlying Pathology and Their Clinical Significance. Int J Mol Sci 2023; 24:ijms24032044. [PMID: 36768367 PMCID: PMC9917178 DOI: 10.3390/ijms24032044] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
α-Synucleinopathies comprise a group of neurodegenerative diseases characterized by altered accumulation of a protein called α-synuclein inside neurons and glial cells. This aggregation leads to the formation of intraneuronal inclusions, Lewy bodies, that constitute the hallmark of α-synuclein pathology. The most prevalent α-synucleinopathies are Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA). To date, only symptomatic treatment is available for these disorders, hence new approaches to their therapy are needed. It has been observed that GBA1 mutations are one of the most impactful risk factors for developing α-synucleinopathies such as PD and DLB. Mutations in the GBA1 gene, which encodes a lysosomal hydrolase β-glucocerebrosidase (GCase), cause a reduction in GCase activity and impaired α-synuclein metabolism. The most abundant GBA1 gene mutations are N370S or N409S, L444P/L483P and E326K/E365K. The mechanisms by which GCase impacts α-synuclein aggregation are poorly understood and need to be further investigated. Here, we discuss some of the potential interactions between α-synuclein and GCase and show how GBA1 mutations may impact the course of the most prevalent α-synucleinopathies.
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Guerre P, Matard-Mann M, Nyvall Collén P. Targeted sphingolipid analysis in chickens suggests different mechanisms of fumonisin toxicity in kidney, lung, and brain. Food Chem Toxicol 2022; 170:113467. [DOI: 10.1016/j.fct.2022.113467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/16/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
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Grabowski GA, Mistry PK. Therapies for lysosomal storage diseases: Principles, practice, and prospects for refinements based on evolving science. Mol Genet Metab 2022; 137:81-91. [PMID: 35933791 DOI: 10.1016/j.ymgme.2022.07.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 12/25/2022]
Affiliation(s)
- Gregory A Grabowski
- University of Cincinnati College of Medicine, Department of Pediatrics, Department of Molecular Genetics, Biochemistry and Microbiology, United States of America; Division of Human Genetics, Cincinnati Children's Hospital Research Foundation, Cincinnati, OH, United States of America.
| | - Pramod K Mistry
- Yale School of Medicine, Department of Medicine, Department of Pediatrics, Department of Cellular & Molecular Physiology, New Haven, CT, United States of America
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Leal AF, Suarez DA, Echeverri-Peña OY, Albarracín SL, Alméciga-Díaz CJ, Espejo-Mojica ÁJ. Sphingolipids and their role in health and disease in the central nervous system. Adv Biol Regul 2022; 85:100900. [PMID: 35870382 DOI: 10.1016/j.jbior.2022.100900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/21/2022] [Accepted: 07/11/2022] [Indexed: 12/22/2022]
Abstract
Sphingolipids (SLs) are lipids derived from sphingosine, and their metabolism involves a broad and complex network of reactions. Although SLs are widely distributed in the body, it is well known that they are present in high concentrations within the central nervous system (CNS). Under physiological conditions, their abundance and distribution in the CNS depend on brain development and cell type. Consequently, SLs metabolism impairment may have a significant impact on the normal CNS function, and has been associated with several disorders, including sphingolipidoses, Parkinson's, and Alzheimer's. This review summarizes the main SLs characteristics and current knowledge about synthesis, catabolism, regulatory pathways, and their role in physiological and pathological scenarios in the CNS.
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Affiliation(s)
- Andrés Felipe Leal
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C, Colombia
| | - Diego A Suarez
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C, Colombia
| | - Olga Yaneth Echeverri-Peña
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C, Colombia
| | - Sonia Luz Albarracín
- Nutrition and Biochemistry Department, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C, Colombia
| | - Carlos Javier Alméciga-Díaz
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C, Colombia.
| | - Ángela Johana Espejo-Mojica
- Institute for the Study of Inborn Errors of Metabolism, Faculty of Science, Pontificia Universidad Javeriana, Bogotá D.C, Colombia.
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