1
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Soraci L, Corsonello A, Paparazzo E, Montesanto A, Piacenza F, Olivieri F, Gambuzza ME, Savedra EV, Marino S, Lattanzio F, Biscetti L. Neuroinflammaging: A Tight Line Between Normal Aging and Age-Related Neurodegenerative Disorders. Aging Dis 2024; 15:1726-1747. [PMID: 38300639 PMCID: PMC11272206 DOI: 10.14336/ad.2023.1001] [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: 08/12/2023] [Accepted: 10/01/2023] [Indexed: 02/02/2024] Open
Abstract
Aging in the healthy brain is characterized by a low-grade, chronic, and sterile inflammatory process known as neuroinflammaging. This condition, mainly consisting in an up-regulation of the inflammatory response at the brain level, contributes to the pathogenesis of age-related neurodegenerative disorders. Development of this proinflammatory state involves the interaction between genetic and environmental factors, able to induce age-related epigenetic modifications. Indeed, the exposure to environmental compounds, drugs, and infections, can contribute to epigenetic modifications of DNA methylome, histone fold proteins, and nucleosome positioning, leading to epigenetic modulation of neuroinflammatory responses. Furthermore, some epigenetic modifiers, which combine and interact during the life course, can contribute to modeling of epigenome dynamics to sustain, or dampen the neuroinflammatory phenotype. The aim of this review is to summarize current knowledge about neuroinflammaging with a particular focus on epigenetic mechanisms underlying the onset and progression of neuroinflammatory cascades in the central nervous system; furthermore, we describe some diagnostic biomarkers that may contribute to increase diagnostic accuracy and help tailor therapeutic strategies in patients with neurodegenerative diseases.
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Affiliation(s)
- Luca Soraci
- Unit of Geriatric Medicine, Italian National Research Center of Aging (IRCCS INRCA), Cosenza, Italy.
| | - Andrea Corsonello
- Unit of Geriatric Medicine, Italian National Research Center of Aging (IRCCS INRCA), Cosenza, Italy.
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy.
| | - Ersilia Paparazzo
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy.
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy.
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, Italian National Research Center of Aging (IRCCS INRCA), IRCCS INRCA, Ancona, Italy.
| | - Fabiola Olivieri
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy.
- Clinic of Laboratory and Precision Medicine, Italian National Research Center of Aging (IRCCS INRCA), Ancona, Italy.
| | | | | | - Silvia Marino
- IRCCS Centro Neurolesi "Bonino-Pulejo”, Messina, Italy.
| | | | - Leonardo Biscetti
- Section of Neurology, Italian National Research Center on Aging (IRCCS INRCA), Ancona, Italy.
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2
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Kim IB, Kim MH, Jung S, Kim WK, Lee J, Ju YS, Webster MJ, Kim S, Kim JH, Kim HJ, Kim J, Kim S, Lee JH. Low-level brain somatic mutations in exonic regions are collectively implicated in autism with germline mutations in autism risk genes. Exp Mol Med 2024:10.1038/s12276-024-01284-1. [PMID: 39085355 DOI: 10.1038/s12276-024-01284-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 04/15/2024] [Accepted: 05/12/2024] [Indexed: 08/02/2024] Open
Abstract
Low-level somatic mutations in the human brain are implicated in various neurological disorders. The contribution of low-level brain somatic mutations to autism spectrum disorder (ASD), however, remains poorly understood. Here, we performed high-depth exome sequencing with an average read depth of 559.3x in 181 cortical, cerebellar, and peripheral tissue samples to identify brain somatic single nucleotide variants (SNVs) in 24 ASD subjects and 31 controls. We detected ~2.4 brain somatic SNVs per exome per single brain region, with a variant allele frequency (VAF) as low as 0.3%. The mutational profiles, including the number, signature, and type, were not significantly different between the ASD patients and controls. Intriguingly, when considering genes with low-level brain somatic SNVs and ASD risk genes with damaging germline SNVs together, the merged set of genes carrying either somatic or germline SNVs in ASD patients was significantly involved in ASD-associated pathophysiology, including dendrite spine morphogenesis (p = 0.025), mental retardation (p = 0.012), and intrauterine growth retardation (p = 0.012). Additionally, the merged gene set showed ASD-associated spatiotemporal expression in the early and mid-fetal cortex, striatum, and thalamus (all p < 0.05). Patients with damaging mutations in the merged gene set had a greater ASD risk than did controls (odds ratio = 3.92, p = 0.025, 95% confidence interval = 1.12-14.79). The findings of this study suggest that brain somatic SNVs and germline SNVs may collectively contribute to ASD-associated pathophysiology.
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Affiliation(s)
- Il Bin Kim
- Department of Psychiatry, CHA Gangnam Medical Center, CHA University School of Medicine, Seoul, 06135, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Myeong-Heui Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Saehoon Jung
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Woo Kyeong Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Junehawk Lee
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Maree J Webster
- Stanley Medical Research Institute, Laboratory of Brain Research, 9800 Medical Center Drive, Suite C-050, Rockville, MD, 20850, USA
| | - Sanghyeon Kim
- Stanley Medical Research Institute, Laboratory of Brain Research, 9800 Medical Center Drive, Suite C-050, Rockville, MD, 20850, USA
| | - Ja Hye Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, 05505, Republic of Korea
| | - Hyun Jung Kim
- Department of Anatomy, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Junho Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
- SoVarGen, SoVarGen, Inc., Daejeon, 34141, Republic of Korea.
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3
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De Meulemeester AS, Reid C, Auvin S, Carlen PL, Cole AJ, Szlendak R, Di Sapia R, Moshé SL, Sankar R, O'Brien TJ, Baulac S, Henshall DC, Akman Ö, Galanopoulou AS. WONOEP appraisal: Modeling early onset epilepsies. Epilepsia 2024. [PMID: 39042520 DOI: 10.1111/epi.18063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/25/2024]
Abstract
Epilepsy has a peak incidence during the neonatal to early childhood period. These early onset epilepsies may be severe conditions frequently associated with comorbidities such as developmental deficits and intellectual disability and, in a significant percentage of patients, may be medication-resistant. The use of adult rodent models in the exploration of mechanisms and treatments for early life epilepsies is challenging, as it ignores significant age-specific developmental differences. More recently, models developed in immature animals, such as rodent pups, or in three-dimensional organoids may more closely model aspects of the immature brain and could result in more translatable findings. Although models are not perfect, they may offer a more controlled screening platform in studies of mechanisms and treatments, which cannot be done in pediatric patient cohorts. On the other hand, more simplified models with higher throughput capacities are required to deal with the large number of epilepsy candidate genes and the need for new treatment options. Therefore, a combination of different modeling approaches will be beneficial in addressing the unmet needs of pediatric epilepsy patients. In this review, we summarize the discussions on this topic that occurred during the XVI Workshop on Neurobiology of Epilepsy, organized in 2022 by the Neurobiology Commission of the International League Against Epilepsy. We provide an overview of selected models of early onset epilepsies, discussing their advantages and disadvantages. Heterologous expression models provide initial functional insights, and zebrafish, rodent models, and brain organoids present increasingly complex platforms for modeling and validating epilepsy-related phenomena. Together, these models offer valuable insights into early onset epilepsies and accelerate hypothesis generation and therapy discovery.
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Affiliation(s)
- Ann-Sofie De Meulemeester
- Institut du Cerveau-Paris Brain Institute-ICM, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS, Sorbonne Université, Paris, France
- Laboratory for Molecular Biodiscovery, KU Leuven, Leuven, Belgium
| | - Christopher Reid
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, Australia
- Department of Medicine, Epilepsy Research Centre, Austin Health, University of Melbourne, Heidelberg, Victoria, Australia
| | - Stéphane Auvin
- Pediatric Neurology Department, CRMR Épilepsies Rares, EpiCARE member, AP-HP, Robert-Debré University Hospital, Paris, France
- INSERM NeuroDiderot, Université Paris Cité, Paris, France
- Institut Universitaire de France, Paris, France
| | - Peter L Carlen
- Krembil Research Institute, Toronto, Ontario, Canada
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Medicine and Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Andrew J Cole
- MGH Epilepsy Service, Division of Clinical Neurophysiology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Roza Szlendak
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
- Institut de Génomique Fonctionnelle, University of Montpellier, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier, France
| | - Rossella Di Sapia
- Department of Acute Brain and Cardiovascular Injury, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Solomon L Moshé
- Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, USA
- Isabelle Rapin Division of Child Neurology, Albert Einstein College of Medicine, Bronx, New York, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Raman Sankar
- Department of Neurology and Pediatrics, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Terence J O'Brien
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria, Australia
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Hospital, Melbourne, Victoria, Australia
| | - Stéphanie Baulac
- Institut du Cerveau-Paris Brain Institute-ICM, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS, Sorbonne Université, Paris, France
| | - David C Henshall
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland (RCSI) University of Medicine and Health Sciences, Dublin, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland (RCSI) University of Medicine and Health Sciences, Dublin, Ireland
| | - Özlem Akman
- Department of Physiology, Faculty of Medicine, Demiroglu Bilim University, Istanbul, Turkey
| | - Aristea S Galanopoulou
- Saul R. Korey Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, USA
- Isabelle Rapin Division of Child Neurology, Albert Einstein College of Medicine, Bronx, New York, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, USA
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4
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Dwivedi R, Kaushik M, Tripathi M, Dada R, Tiwari P. Unraveling the genetic basis of epilepsy: Recent advances and implications for diagnosis and treatment. Brain Res 2024; 1843:149120. [PMID: 39032529 DOI: 10.1016/j.brainres.2024.149120] [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: 05/20/2024] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 07/23/2024]
Abstract
Epilepsy, affecting approximately 1% of the global population, manifests as recurring seizures and is heavily influenced by genetic factors. Recent advancements in genetic technologies have revolutionized our understanding of epilepsy's genetic landscape. Key studies, such as the discovery of mutations in ion channels (e.g., SCN1A and SCN2A), neurotransmitter receptors (e.g., GABRA1), and synaptic proteins (e.g., SYNGAP1, KCNQ2), have illuminated critical pathways underlying epilepsy susceptibility and pathogenesis. Genome-wide association studies (GWAS) have identified specific genetic variations linked to epilepsy risk, such as variants near SCN1A and PCDH7, enhancing diagnostic accuracy and enabling personalized treatment strategies. Moreover, epigenetic mechanisms, including DNA methylation (e.g., MBD5), histone modifications (e.g., HDACs), and non-coding RNAs (e.g., miR-134), play pivotal roles in altering gene expression and synaptic plasticity, contributing to epileptogenesis. These discoveries offer promising avenues for therapeutic interventions aimed at improving outcomes for epilepsy patients. Genetic testing has become essential in clinical practice, facilitating precise diagnosis and tailored management approaches based on individual genetic profiles. Furthermore, insights into epigenetic regulation suggest novel therapeutic targets for developing more effective epilepsy treatments. In summary, this review highlights significant progress in understanding the genetic and epigenetic foundations of epilepsy. By integrating findings from key studies and specifying genes involved in epigenetic modifications, we underscore the potential for advanced therapeutic strategies in this complex neurological disorder, emphasizing the importance of personalized medicine approaches in epilepsy management.
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Affiliation(s)
- Rekha Dwivedi
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Meenakshi Kaushik
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Manjari Tripathi
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Rima Dada
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Prabhakar Tiwari
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India.
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5
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Bohaczuk SC, Amador ZJ, Li C, Mallory BJ, Swanson EG, Ranchalis J, Vollger MR, Munson KM, Walsh T, Hamm MO, Mao Y, Lieber A, Stergachis AB. Resolving the chromatin impact of mosaic variants with targeted Fiber-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.09.602608. [PMID: 39026856 PMCID: PMC11257596 DOI: 10.1101/2024.07.09.602608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Accurately quantifying the functional consequences of non-coding mosaic variants requires the pairing of DNA sequence with both accessible and closed chromatin architectures along individual DNA molecules-a pairing that cannot be achieved using traditional fragmentation-based chromatin assays. We demonstrate that targeted single-molecule chromatin fiber sequencing (Fiber-seq) achieves this, permitting single-molecule, long-read genomic and epigenomic profiling across targeted >100 kilobase loci with ~10-fold enrichment over untargeted sequencing. Targeted Fiber-seq reveals that pathogenic expansions of the DMPK CTG repeat that underlie Myotonic Dystrophy 1 are characterized by somatic instability and disruption of multiple nearby regulatory elements, both of which are repeat length-dependent. Furthermore, we reveal that therapeutic adenine base editing of the segmentally duplicated γ-globin (HBG1/HBG2) promoters in primary human hematopoietic cells induced towards an erythroblast lineage increases the accessibility of the HBG1 promoter as well as neighboring regulatory elements. Overall, we find that these non-protein coding mosaic variants can have complex impacts on chromatin architectures, including extending beyond the regulatory element harboring the variant.
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Affiliation(s)
- Stephanie C. Bohaczuk
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Zachary J. Amador
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Chang Li
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Elliott G. Swanson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jane Ranchalis
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Mitchell R. Vollger
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Tom Walsh
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Morgan O. Hamm
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Yizi Mao
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Andre Lieber
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrew B. Stergachis
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA USA
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6
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Pengo M, Squitieri F. Beyond CAG Repeats: The Multifaceted Role of Genetics in Huntington Disease. Genes (Basel) 2024; 15:807. [PMID: 38927742 PMCID: PMC11203031 DOI: 10.3390/genes15060807] [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: 05/01/2024] [Revised: 06/11/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Huntington disease (HD) is a dominantly inherited neurodegenerative disorder caused by a CAG expansion on the huntingtin (HTT) gene and is characterized by progressive motor, cognitive, and neuropsychiatric decline. Recently, new genetic factors besides CAG repeats have been implicated in the disease pathogenesis. Most genetic modifiers are involved in DNA repair pathways and, as the cause of the loss of CAA interruption in the HTT gene, they exert their main influence through somatic expansion. However, this mechanism might not be the only driver of HD pathogenesis, and future studies are warranted in this field. The aim of the present review is to dissect the many faces of genetics in HD pathogenesis, from cis- and trans-acting genetic modifiers to RNA toxicity, mitochondrial DNA mutations, and epigenetics factors. Exploring genetic modifiers of HD onset and progression appears crucial to elucidate not only disease pathogenesis, but also to improve disease prediction and prevention, develop biomarkers of disease progression and response to therapies, and recognize new therapeutic opportunities. Since the same genetic mechanisms are also described in other repeat expansion diseases, their implications might encompass the whole spectrum of these disorders.
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Affiliation(s)
- Marta Pengo
- Department of Molecular and Translational Medicine, University of Brescia, 25121 Brescia, Italy;
| | - Ferdinando Squitieri
- Centre for Neurological Rare Diseases (CMNR), Fondazione Lega Italiana Ricerca Huntington (LIRH), 00161 Rome, Italy
- Huntington and Rare Diseases Unit, IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy
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7
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Tai NC, Shinmyo Y, Kawasaki H. Astrocyte diversity in the ferret cerebrum revealed with astrocyte-specific genetic manipulation. Glia 2024. [PMID: 38884631 DOI: 10.1002/glia.24587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 06/18/2024]
Abstract
Astrocytes in the cerebrum play important roles such as the regulation of synaptic functions, homeostasis, water transport, and the blood-brain barrier. It has been proposed that astrocytes in the cerebrum acquired diversity and developed functionally during evolution. Here, we show that like human astrocytes, ferret astrocytes in the cerebrum exhibit various morphological subtypes which mice do not have. We found that layer 1 of the ferret cerebrum contained not only protoplasmic astrocytes but also pial interlaminar astrocytes and subpial interlaminar astrocytes. Morphologically polarized astrocytes, which have a long unbranched process, were found in layer 6. Like human white matter, ferret white matter exhibited four subtypes of astrocytes. Furthermore, our quantification showed that ferret astrocytes had a larger territory size and a longer radius length than mouse astrocytes. Thus, our results indicate that, similar to the human cerebrum, the ferret cerebrum has a well-developed diversity of astrocytes. Ferrets should be useful for investigating the molecular and cellular mechanisms leading to astrocyte diversity, the functions of each astrocyte subtype and the involvement of different astrocyte subtypes in various neurological diseases.
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Affiliation(s)
- Nguyen Chi Tai
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
- Sapiens Life Sciences, Evolution and Medicine Research Center, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Yohei Shinmyo
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
- Department of Neurophysiology, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Hiroshi Kawasaki
- Department of Medical Neuroscience, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, Japan
- Sapiens Life Sciences, Evolution and Medicine Research Center, Kanazawa University, Kanazawa, Ishikawa, Japan
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8
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Mato-Blanco X, Kim SK, Jourdon A, Ma S, Tebbenkamp AT, Liu F, Duque A, Vaccarino FM, Sestan N, Colantuoni C, Rakic P, Santpere G, Micali N. Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.598925. [PMID: 38915580 PMCID: PMC11195173 DOI: 10.1101/2024.06.14.598925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The implications of the early phases of human telencephalic development, involving neural stem cells (NSCs), in the etiology of cortical disorders remain elusive. Here, we explored the expression dynamics of cortical and neuropsychiatric disorder-associated genes in datasets generated from human NSCs across telencephalic fate transitions in vitro and in vivo. We identified risk genes expressed in brain organizers and sequential gene regulatory networks across corticogenesis revealing disease-specific critical phases, when NSCs are more vulnerable to gene dysfunctions, and converging signaling across multiple diseases. Moreover, we simulated the impact of risk transcription factor (TF) depletions on different neural cell types spanning the developing human neocortex and observed a spatiotemporal-dependent effect for each perturbation. Finally, single-cell transcriptomics of newly generated autism-affected patient-derived NSCs in vitro revealed recurrent alterations of TFs orchestrating brain patterning and NSC lineage commitment. This work opens new perspectives to explore human brain dysfunctions at the early phases of development.
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Affiliation(s)
- Xoel Mato-Blanco
- Hospital del Mar Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia, Spain
| | - Suel-Kee Kim
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Alexandre Jourdon
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Fuchen Liu
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Alvaro Duque
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Flora M. Vaccarino
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
- Departments of Psychiatry, Genetics and Comparative Medicine, Wu Tsai Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Carlo Colantuoni
- Depts. of Neurology, Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Pasko Rakic
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Gabriel Santpere
- Hospital del Mar Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia, Spain
| | - Nicola Micali
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
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9
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Graham JH, Schlachetzki JCM, Yang X, Breuss MW. Genomic Mosaicism of the Brain: Origin, Impact, and Utility. Neurosci Bull 2024; 40:759-776. [PMID: 37898991 PMCID: PMC11178748 DOI: 10.1007/s12264-023-01124-8] [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: 05/04/2023] [Accepted: 07/16/2023] [Indexed: 10/31/2023] Open
Abstract
Genomic mosaicism describes the phenomenon where some but not all cells within a tissue harbor unique genetic mutations. Traditionally, research focused on the impact of genomic mosaicism on clinical phenotype-motivated by its involvement in cancers and overgrowth syndromes. More recently, we increasingly shifted towards the plethora of neutral mosaic variants that can act as recorders of cellular lineage and environmental exposures. Here, we summarize the current state of the field of genomic mosaicism research with a special emphasis on our current understanding of this phenomenon in brain development and homeostasis. Although the field of genomic mosaicism has a rich history, technological advances in the last decade have changed our approaches and greatly improved our knowledge. We will provide current definitions and an overview of contemporary detection approaches for genomic mosaicism. Finally, we will discuss the impact and utility of genomic mosaicism.
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Affiliation(s)
- Jared H Graham
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, 92093-0021, San Diego, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, 92123, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, 80045-2581, CO, USA.
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10
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Carey AR, Miller NR, Cui H, Allis K, Balog A, Bai R, Vernon HJ. Myopathy and Ophthalmologic Abnormalities in Association With Multiple Skeletal Muscle Mitochondrial DNA Deletions. J Neuroophthalmol 2024; 44:247-252. [PMID: 37665646 DOI: 10.1097/wno.0000000000001984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
BACKGROUND Establishing a molecular diagnosis of mitochondrial diseases due to pathogenic mitochondrial DNA (mtDNA) variants can be difficult because of varying levels of tissue heteroplasmy, and identifying these variants is important for clinical management. Here, we present clinical and molecular findings in 8 adult patients with classical features of mitochondrial ophthalmologic and/or muscle disease and multiple mtDNA deletions isolated to muscle. METHODS The patients were identified via a retrospective review of patients seen in both a tertiary ophthalmology center and a genetics clinic with a clinical diagnosis of chronic progressive external ophthalmoplegia, optic nerve abnormalities, and/or mitochondrial myopathy. Age at onset of symptoms ranged from 18 to 61 years. Ocular manifestations included bilateral optic neuropathy in one patient, bilateral optic disc cupping without optic neuropathy in 2 patients, ptosis in 4 patients, and ocular motility deficits in 2 patients. Five patients had generalized weakness. RESULTS Pathogenic variants in mtDNA were not found in the blood or buccal sample from any patient, but 7 of 8 patients had multiple mtDNA deletions identified in muscle tissue. One patient had a single mtDNA deletion identified in the muscle. Heteroplasmy was less than 15% for all of the identified deletions, with the exception of one deletion that had a heteroplasmy of 50%-60%. None of the patients were found to have a nuclear gene variant known to be associated with mitochondrial DNA maintenance. CONCLUSIONS mtDNA deletions were identified in adult patients with ophthalmologic and/or musle abnormalities and may underlie their clinical presentations.
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Affiliation(s)
- Andrew R Carey
- Neuro-Ophthalmology Division (ARC, NRM), Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland; GeneDx (HC, KA, AB, RB), Gaithersburg, Maryland; and Department of Genetic Medicine (HJV), Johns Hopkins University School of Medicine, Baltimore, Maryland
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11
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Zhang X, Celic I, Mitchell H, Stuckert S, Vedula L, Han J. Comprehensive profiling of L1 retrotransposons in mouse. Nucleic Acids Res 2024; 52:5166-5178. [PMID: 38647072 PMCID: PMC11109951 DOI: 10.1093/nar/gkae273] [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: 11/13/2023] [Revised: 03/25/2024] [Accepted: 04/06/2024] [Indexed: 04/25/2024] Open
Abstract
L1 elements are retrotransposons currently active in mammals. Although L1s are typically silenced in most normal tissues, elevated L1 expression is associated with a variety of conditions, including cancer, aging, infertility and neurological disease. These associations have raised interest in the mapping of human endogenous de novo L1 insertions, and a variety of methods have been developed for this purpose. Adapting these methods to mouse genomes would allow us to monitor endogenous in vivo L1 activity in controlled, experimental conditions using mouse disease models. Here, we use a modified version of transposon insertion profiling, called nanoTIPseq, to selectively enrich young mouse L1s. By linking this amplification step with nanopore sequencing, we identified >95% annotated L1s from C57BL/6 genomic DNA using only 200 000 sequencing reads. In the process, we discovered 82 unannotated L1 insertions from a single C57BL/6 genome. Most of these unannotated L1s were near repetitive sequence and were not found with short-read TIPseq. We used nanoTIPseq on individual mouse breast cancer cells and were able to identify the annotated and unannotated L1s, as well as new insertions specific to individual cells, providing proof of principle for using nanoTIPseq to interrogate retrotransposition activity at the single-cell level in vivo.
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Affiliation(s)
- Xuanming Zhang
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Ivana Celic
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Hannah Mitchell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Sam Stuckert
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Lalitha Vedula
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jeffrey S Han
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA 70112, USA
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12
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Jiang L, Jia L, Wang Y, Wu Y, Yue J. Adap-BDCM: Adaptive Bilinear Dynamic Cascade Model for Classification Tasks on CNV Datasets. Interdiscip Sci 2024:10.1007/s12539-024-00635-w. [PMID: 38758306 DOI: 10.1007/s12539-024-00635-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
Copy number variation (CNV) is an essential genetic driving factor of cancer formation and progression, making intelligent classification based on CNV feasible. However, there are a few challenges in the current machine learning and deep learning methods, such as the design of base classifier combination schemes in ensemble methods and the selection of layers of neural networks, which often result in low accuracy. Therefore, an adaptive bilinear dynamic cascade model (Adap-BDCM) is developed to further enhance the accuracy and applicability of these methods for intelligent classification on CNV datasets. In this model, a feature selection module is introduced to mitigate the interference of redundant information, and a bilinear model based on the gated attention mechanism is proposed to extract more beneficial deep fusion features. Furthermore, an adaptive base classifier selection scheme is designed to overcome the difficulty of manually designing base classifier combinations and enhance the applicability of the model. Lastly, a novel feature fusion scheme with an attribute recall submodule is constructed, effectively avoiding getting stuck in local solutions and missing some valuable information. Numerous experiments have demonstrated that our Adap-BDCM model exhibits optimal performance in cancer classification, stage prediction, and recurrence on CNV datasets. This study can assist physicians in making diagnoses faster and better.
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Affiliation(s)
- Liancheng Jiang
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, 030600, China
| | - Liye Jia
- College of Computer Science and Technology, Taiyuan Normal University, Taiyuan, 030619, China
| | - Yizhen Wang
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, 030600, China
| | - Yongfei Wu
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, 030600, China
| | - Junhong Yue
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, 030600, China.
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13
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Carton RJ, Doyle MG, Kearney H, Steward CA, Lench NJ, Rogers A, Heinzen EL, McDonald S, Fay J, Lacey A, Beausang A, Cryan J, Brett F, El-Naggar H, Widdess-Walsh P, Costello D, Kilbride R, Doherty CP, Sweeney KJ, O'Brien DF, Henshall DC, Delanty N, Cavalleri GL, Benson KA. Somatic variants as a cause of drug-resistant epilepsy including mesial temporal lobe epilepsy with hippocampal sclerosis. Epilepsia 2024; 65:1451-1461. [PMID: 38491957 DOI: 10.1111/epi.17943] [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: 05/29/2023] [Revised: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 03/18/2024]
Abstract
OBJECTIVE The contribution of somatic variants to epilepsy has recently been demonstrated, particularly in the etiology of malformations of cortical development. The aim of this study was to determine the diagnostic yield of somatic variants in genes that have been previously associated with a somatic or germline epilepsy model, ascertained from resected brain tissue from patients with multidrug-resistant focal epilepsy. METHODS Forty-two patients were recruited across three categories: (1) malformations of cortical development, (2) mesial temporal lobe epilepsy with hippocampal sclerosis, and (3) nonlesional focal epilepsy. Participants were subdivided based on histopathology of the resected brain. Paired blood- and brain-derived DNA samples were sequenced using high-coverage targeted next generation sequencing to high depth (585× and 1360×, respectively). Variants were identified using Genome Analysis ToolKit (GATK4) MuTect-2 and confirmed using high-coverage Amplicon-EZ sequencing. RESULTS Sequence data on 41 patients passed quality control. Four somatic variants were validated following amplicon sequencing: within CBL, ALG13, MTOR, and FLNA. The diagnostic yield across 41 patients was 10%, 9% in mesial temporal lobe epilepsy with hippocampal sclerosis and 20% in malformations of cortical development. SIGNIFICANCE This study provides novel insights into the etiology of mesial temporal lobe epilepsy with hippocampal sclerosis, highlighting a potential pathogenic role of somatic variants in CBL and ALG13. We also report candidate diagnostic somatic variants in FLNA in focal cortical dysplasia, while providing further insight into the importance of MTOR and related genes in focal cortical dysplasia. This work demonstrates the potential molecular diagnostic value of variants in both germline and somatic epilepsy genes.
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Affiliation(s)
- Robert J Carton
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Michael G Doyle
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
- Strategic Academic Recruitment Doctor of Medicine Programme, Royal College of Surgeons in Ireland in collaboration with Blackrock Clinic, Dublin, Ireland
| | - Hugh Kearney
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | | | | | - Anthony Rogers
- Congenica Limited, BioData Innovation Centre, Cambridge, UK
| | - Erin L Heinzen
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Seamus McDonald
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Joanna Fay
- Royal College of Surgeons in Ireland Biobanking Service, Dublin, Ireland
| | - Austin Lacey
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Alan Beausang
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Francesca Brett
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Hany El-Naggar
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Peter Widdess-Walsh
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Daniel Costello
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Neurology, Cork University Hospital, Cork, Ireland
| | - Ronan Kilbride
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Colin P Doherty
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Neurology, St. James's Hospital, Dublin, Ireland
| | - Kieron J Sweeney
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Donncha F O'Brien
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - David C Henshall
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Norman Delanty
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Gianpiero L Cavalleri
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Katherine A Benson
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
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14
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Cheng YHH, Bohaczuk SC, Stergachis AB. Functional categorization of gene regulatory variants that cause Mendelian conditions. Hum Genet 2024; 143:559-605. [PMID: 38436667 PMCID: PMC11078748 DOI: 10.1007/s00439-023-02639-w] [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: 06/21/2023] [Accepted: 12/30/2023] [Indexed: 03/05/2024]
Abstract
Much of our current understanding of rare human diseases is driven by coding genetic variants. However, non-coding genetic variants play a pivotal role in numerous rare human diseases, resulting in diverse functional impacts ranging from altered gene regulation, splicing, and/or transcript stability. With the increasing use of genome sequencing in clinical practice, it is paramount to have a clear framework for understanding how non-coding genetic variants cause disease. To this end, we have synthesized the literature on hundreds of non-coding genetic variants that cause rare Mendelian conditions via the disruption of gene regulatory patterns and propose a functional classification system. Specifically, we have adapted the functional classification framework used for coding variants (i.e., loss-of-function, gain-of-function, and dominant-negative) to account for features unique to non-coding gene regulatory variants. We identify that non-coding gene regulatory variants can be split into three distinct categories by functional impact: (1) non-modular loss-of-expression (LOE) variants; (2) modular loss-of-expression (mLOE) variants; and (3) gain-of-ectopic-expression (GOE) variants. Whereas LOE variants have a direct corollary with coding loss-of-function variants, mLOE and GOE variants represent disease mechanisms that are largely unique to non-coding variants. These functional classifications aim to provide a unified terminology for categorizing the functional impact of non-coding variants that disrupt gene regulatory patterns in Mendelian conditions.
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Affiliation(s)
- Y H Hank Cheng
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Stephanie C Bohaczuk
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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15
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Omidsalar AA, McCullough CG, Xu L, Boedijono S, Gerke D, Webb MG, Manojlovic Z, Sequeira A, Lew MF, Santorelli M, Serrano GE, Beach TG, Limon A, Vawter MP, Hjelm BE. Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets. Commun Biol 2024; 7:200. [PMID: 38368460 PMCID: PMC10874445 DOI: 10.1038/s42003-024-05877-4] [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: 03/15/2023] [Accepted: 01/31/2024] [Indexed: 02/19/2024] Open
Abstract
Common mitochondrial DNA (mtDNA) deletions are large structural variants in the mitochondrial genome that accumulate in metabolically active tissues with age and have been investigated in various diseases. We applied the Splice-Break2 pipeline (designed for high-throughput quantification of mtDNA deletions) to human RNA-Seq datasets and describe the methodological considerations for evaluating common deletions in bulk, single-cell, and spatial transcriptomics datasets. A robust evaluation of 1570 samples from 14 RNA-Seq studies showed: (i) the abundance of some common deletions detected in PCR-amplified mtDNA correlates with levels observed in RNA-Seq data; (ii) RNA-Seq library preparation method has a strong effect on deletion detection; (iii) deletions had a significant, positive correlation with age in brain and muscle; (iv) deletions were enriched in cortical grey matter, specifically in layers 3 and 5; and (v) brain regions with dopaminergic neurons (i.e., substantia nigra, ventral tegmental area, and caudate nucleus) had remarkable enrichment of common mtDNA deletions.
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Affiliation(s)
- Audrey A Omidsalar
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Carmel G McCullough
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Lili Xu
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Stanley Boedijono
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Daniel Gerke
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Michelle G Webb
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Zarko Manojlovic
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Adolfo Sequeira
- Department of Psychiatry and Human Behavior, University of California - Irvine (UCI) School of Medicine, Irvine, CA, USA
| | - Mark F Lew
- Department of Neurology, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Marco Santorelli
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Geidy E Serrano
- Banner Sun Health Research Institute (BSHRI), Sun City, AZ, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute (BSHRI), Sun City, AZ, USA
| | - Agenor Limon
- Mitchell Center for Neurodegenerative Diseases, Department of Neurology, School of Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Marquis P Vawter
- Department of Psychiatry and Human Behavior, University of California - Irvine (UCI) School of Medicine, Irvine, CA, USA
| | - Brooke E Hjelm
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA.
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16
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Fukuda K. The role of transposable elements in human evolution and methods for their functional analysis: current status and future perspectives. Genes Genet Syst 2024; 98:289-304. [PMID: 37866889 DOI: 10.1266/ggs.23-00140] [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] [Indexed: 10/24/2023] Open
Abstract
Transposable elements (TEs) are mobile DNA sequences that can insert themselves into various locations within the genome, causing mutations that may provide advantages or disadvantages to individuals and species. The insertion of TEs can result in genetic variation that may affect a wide range of human traits including genetic disorders. Understanding the role of TEs in human biology is crucial for both evolutionary and medical research. This review discusses the involvement of TEs in human traits and disease susceptibility, as well as methods for functional analysis of TEs.
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Affiliation(s)
- Kei Fukuda
- Integrative Genomics Unit, The University of Melbourne
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17
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Mishra SK, Nelson CW, Zhu B, Pinheiro M, Lee HJ, Dean M, Burdett L, Yeager M, Mirabello L. Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus. Virus Evol 2024; 10:veae013. [PMID: 38455683 PMCID: PMC10919477 DOI: 10.1093/ve/veae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 03/09/2024] Open
Abstract
High-coverage sequencing allows the study of variants occurring at low frequencies within samples, but is susceptible to false-positives caused by sequencing error. Ion Torrent has a very low single nucleotide variant (SNV) error rate and has been employed for the majority of human papillomavirus (HPV) whole genome sequences. However, benchmarking of intrahost SNVs (iSNVs) has been challenging, partly due to limitations imposed by the HPV life cycle. We address this problem by deep sequencing three replicates for each of 31 samples of HPV type 18 (HPV18). Errors, defined as iSNVs observed in only one of three replicates, are dominated by C→T (G→A) changes, independently of trinucleotide context. True iSNVs, defined as those observed in all three replicates, instead show a more diverse SNV type distribution, with particularly elevated C→T rates in CCG context (CCG→CTG; CGG→CAG) and C→A rates in ACG context (ACG→AAG; CGT→CTT). Characterization of true iSNVs allowed us to develop two methods for detecting true variants: (1) VCFgenie, a dynamic binomial filtering tool which uses each variant's allele count and coverage instead of fixed frequency cut-offs; and (2) a machine learning binary classifier which trains eXtreme Gradient Boosting models on variant features such as quality and trinucleotide context. Each approach outperforms fixed-cut-off filtering of iSNVs, and performance is enhanced when both are used together. Our results provide improved methods for identifying true iSNVs in within-host applications across sequencing platforms, specifically using HPV18 as a case study.
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Affiliation(s)
- Sambit K Mishra
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Chase W Nelson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Hyo Jung Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Laurie Burdett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Bldg. 430, Frederick, MD 21702, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Rockville, MD 20850, USA
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18
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Ma W, Wu H, Chen Y, Xu H, Jiang J, Du B, Wan M, Ma X, Chen X, Lin L, Su X, Bao X, Shen Y, Xu N, Ruan J, Jiang H, Ding Y. New techniques to identify the tissue of origin for cancer of unknown primary in the era of precision medicine: progress and challenges. Brief Bioinform 2024; 25:bbae028. [PMID: 38343328 PMCID: PMC10859692 DOI: 10.1093/bib/bbae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/10/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Despite a standardized diagnostic examination, cancer of unknown primary (CUP) is a rare metastatic malignancy with an unidentified tissue of origin (TOO). Patients diagnosed with CUP are typically treated with empiric chemotherapy, although their prognosis is worse than those with metastatic cancer of a known origin. TOO identification of CUP has been employed in precision medicine, and subsequent site-specific therapy is clinically helpful. For example, molecular profiling, including genomic profiling, gene expression profiling, epigenetics and proteins, has facilitated TOO identification. Moreover, machine learning has improved identification accuracy, and non-invasive methods, such as liquid biopsy and image omics, are gaining momentum. However, the heterogeneity in prediction accuracy, sample requirements and technical fundamentals among the various techniques is noteworthy. Accordingly, we systematically reviewed the development and limitations of novel TOO identification methods, compared their pros and cons and assessed their potential clinical usefulness. Our study may help patients shift from empirical to customized care and improve their prognoses.
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Affiliation(s)
- Wenyuan Ma
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Wu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiran Chen
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongxia Xu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Junjie Jiang
- Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bang Du
- Real Doctor AI Research Centre, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Mingyu Wan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaolu Ma
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoyu Chen
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lili Lin
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinhui Su
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuanwen Bao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yifei Shen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Nong Xu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian Ruan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiping Jiang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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19
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Oane I, Barborica A, Daneasa A, Maliia MD, Ciurea J, Stoica S, Dabu A, Bratu F, Lentoiu C, Mindruta I. Organization of the epileptogenic zone and signal analysis at seizure onset in patients with drug-resistant epilepsy due to focal cortical dysplasia with mTOR pathway gene mutations-An SEEG study. Epilepsia Open 2023; 8:1588-1595. [PMID: 37574648 PMCID: PMC10690691 DOI: 10.1002/epi4.12810] [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: 04/06/2023] [Accepted: 08/09/2023] [Indexed: 08/15/2023] Open
Abstract
Epilepsy surgery in genetic drug-resistant epilepsy is a debated subject as more histological and molecular data are available. We retrospectively collected data from focal drug-resistant epilepsy patients that underwent stereoelectroencephalography (SEEG) invasive recordings. Patients with nonlesional brain imaging or in whom a first epilepsy surgery failed to control seizures were selected. We computed and displayed the intracranial ictal onset activity pattern on structural imaging. Patients underwent epilepsy gene panel testing, next generation sequencing-NGS. Of 113 patients, 13 underwent genetic testing, and in 6 patients, a mechanistic target of rapamycin pathway gene germline mutation (mTOR) was identified. Brain imaging was nonlesional except for one patient in whom two abnormalities suggestive of focal cortical dysplasia (FCD) were found. Patients underwent tailored brain surgery based on SEEG data, tissue analysis revealed FCD and postsurgical outcome was favorable. Our findings are similar to previous case series suggesting that epilepsy surgery can be a treatment option in patients with mTOR pathway mutation. In patients with mTOR pathway mutation, the postsurgical outcome is favorable if complete resection of the epileptogenic zone is performed. Electrophysiological seizure onset patterns in FCDs associated with mTOR pathway mutations display low-voltage fast activity as previously described.
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Affiliation(s)
- Irina Oane
- Epilepsy Monitoring UnitUniversity Emergency Hospital BucharestBucharestRomania
| | | | - Andrei Daneasa
- Epilepsy Monitoring UnitUniversity Emergency Hospital BucharestBucharestRomania
| | | | - Jean Ciurea
- Neurosurgery Department“Bagdasar‐Arseni” Emergency HospitalBucharestRomania
| | - Sergiu Stoica
- Neurosurgery DepartmentBrain Institute, Monza HospitalBucharestRomania
| | - Aurelia Dabu
- Neurosurgery DepartmentUniversity Emergency Hospital BucharestBucharestRomania
| | - Flavius Bratu
- Epilepsy Monitoring UnitUniversity Emergency Hospital BucharestBucharestRomania
| | - Camelia Lentoiu
- Epilepsy Monitoring UnitUniversity Emergency Hospital BucharestBucharestRomania
| | - Ioana Mindruta
- Epilepsy Monitoring UnitUniversity Emergency Hospital BucharestBucharestRomania
- Neurology Department, Faculty of MedicineUniversity of Medicine and Pharmacy Carol Davila BucharestBucharestRomania
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20
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Zhang P, Chaldebas M, Ogishi M, Al Qureshah F, Ponsin K, Feng Y, Rinchai D, Milisavljevic B, Han JE, Moncada-Vélez M, Keles S, Schröder B, Stenson PD, Cooper DN, Cobat A, Boisson B, Zhang Q, Boisson-Dupuis S, Abel L, Casanova JL. Genome-wide detection of human intronic AG-gain variants located between splicing branchpoints and canonical splice acceptor sites. Proc Natl Acad Sci U S A 2023; 120:e2314225120. [PMID: 37931111 PMCID: PMC10655562 DOI: 10.1073/pnas.2314225120] [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: 08/19/2023] [Accepted: 10/02/2023] [Indexed: 11/08/2023] Open
Abstract
Human genetic variants that introduce an AG into the intronic region between the branchpoint (BP) and the canonical splice acceptor site (ACC) of protein-coding genes can disrupt pre-mRNA splicing. Using our genome-wide BP database, we delineated the BP-ACC segments of all human introns and found extreme depletion of AG/YAG in the [BP+8, ACC-4] high-risk region. We developed AGAIN as a genome-wide computational approach to systematically and precisely pinpoint intronic AG-gain variants within the BP-ACC regions. AGAIN identified 350 AG-gain variants from the Human Gene Mutation Database, all of which alter splicing and cause disease. Among them, 74% created new acceptor sites, whereas 31% resulted in complete exon skipping. AGAIN also predicts the protein-level products resulting from these two consequences. We performed AGAIN on our exome/genomes database of patients with severe infectious diseases but without known genetic etiology and identified a private homozygous intronic AG-gain variant in the antimycobacterial gene SPPL2A in a patient with mycobacterial disease. AGAIN also predicts a retention of six intronic nucleotides that encode an in-frame stop codon, turning AG-gain into stop-gain. This allele was then confirmed experimentally to lead to loss of function by disrupting splicing. We further showed that AG-gain variants inside the high-risk region led to misspliced products, while those outside the region did not, by two case studies in genes STAT1 and IRF7. We finally evaluated AGAIN on our 14 paired exome-RNAseq samples and found that 82% of AG-gain variants in high-risk regions showed evidence of missplicing. AGAIN is publicly available from https://hgidsoft.rockefeller.edu/AGAIN and https://github.com/casanova-lab/AGAIN.
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Affiliation(s)
- Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Matthieu Chaldebas
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Fahd Al Qureshah
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Khoren Ponsin
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Yi Feng
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Baptiste Milisavljevic
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Ji Eun Han
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Marcela Moncada-Vélez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
| | - Sevgi Keles
- Division of Pediatric Allergy and Immunology, Necmettin Erbakan University, Meram Medical Faculty, Konya42080, Turkey
| | - Bernd Schröder
- Institute of Physiological Chemistry, Technische Universität Dresden, Dresden01307, Germany
| | - Peter D. Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, CardiffCF14 4XN, United Kingdom
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, CardiffCF14 4XN, United Kingdom
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY10065
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Paris75015, France
- Paris Cité University, Imagine Institute, Paris75015, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris75015, France
- HHMI, New York, NY10065
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21
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Zhang X, Celic I, Mitchell H, Stuckert S, Vedula L, Han JS. Comprehensive profiling of L1 retrotransposons in mouse. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566638. [PMID: 38014156 PMCID: PMC10680791 DOI: 10.1101/2023.11.13.566638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
L1 elements are retrotransposons currently active in mammals. Although L1s are typically silenced in most normal tissues, elevated L1 expression is associated with a variety of conditions, including cancer, aging, infertility, and neurological disease. These associations have raised interest in the mapping of human endogenous de novo L1 insertions, and a variety of methods have been developed for this purpose. Adapting these methods to mouse genomes would allow us to monitor endogenous in vivo L1 activity in controlled, experimental conditions using mouse disease models. Here we use a modified version of transposon insertion profiling, called nanoTIPseq, to selectively enrich young mouse L1s. By linking this amplification step with nanopore sequencing, we identified >95% annotated L1s from C57BL/6 genomic DNA using only 200,000 sequencing reads. In the process, we discovered 82 unannotated L1 insertions from a single C57BL/6 genome. Most of these unannotated L1s were near repetitive sequence and were not found with short-read TIPseq. We used nanoTIPseq on individual mouse breast cancer cells and were able to identify the annotated and unannotated L1s, as well as new insertions specific to individual cells, providing proof of principle for using nanoTIPseq to interrogate retrotransposition activity at the single cell level in vivo .
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22
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Zhang Y, Zeng J, Xu B. Phenotypic analysis with trans-recombination-based genetic mosaic models. J Biol Chem 2023; 299:105265. [PMID: 37734556 PMCID: PMC10587715 DOI: 10.1016/j.jbc.2023.105265] [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: 07/18/2023] [Revised: 09/01/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
Mosaicism refers to the presence of genetically distinct cell populations in an individual derived from a single zygote, which occurs during the process of development, aging, and genetic diseases. To date, a variety of genetically engineered mosaic analysis models have been established and widely used in studying gene function at exceptional cellular and spatiotemporal resolution, leading to many ground-breaking discoveries. Mosaic analysis with a repressible cellular marker and mosaic analysis with double markers are genetic mosaic analysis models based on trans-recombination. These models can generate sibling cells of distinct genotypes in the same animal and simultaneously label them with different colors. As a result, they offer a powerful approach for lineage tracing and studying the behavior of individual mutant cells in a wildtype environment, which is particularly useful for determining whether gene function is cell autonomous or nonautonomous. Here, we present a comprehensive review on the establishment and applications of mosaic analysis with a repressible cellular marker and mosaic analysis with double marker systems. Leveraging the capabilities of these mosaic models for phenotypic analysis will facilitate new discoveries on the cellular and molecular mechanisms of development and disease.
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Affiliation(s)
- Yu Zhang
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Jianhao Zeng
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Bing Xu
- School of Life Sciences, Nantong University, Nantong, Jiangsu, China.
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23
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Micali N, Ma S, Li M, Kim SK, Mato-Blanco X, Sindhu SK, Arellano JI, Gao T, Shibata M, Gobeske KT, Duque A, Santpere G, Sestan N, Rakic P. Molecular programs of regional specification and neural stem cell fate progression in macaque telencephalon. Science 2023; 382:eadf3786. [PMID: 37824652 PMCID: PMC10705812 DOI: 10.1126/science.adf3786] [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: 10/17/2022] [Accepted: 07/30/2023] [Indexed: 10/14/2023]
Abstract
During early telencephalic development, intricate processes of regional patterning and neural stem cell (NSC) fate specification take place. However, our understanding of these processes in primates, including both conserved and species-specific features, remains limited. Here, we profiled 761,529 single-cell transcriptomes from multiple regions of the prenatal macaque telencephalon. We deciphered the molecular programs of the early organizing centers and their cross-talk with NSCs, revealing primate-biased galanin-like peptide (GALP) signaling in the anteroventral telencephalon. Regional transcriptomic variations were observed along the frontotemporal axis during early stages of neocortical NSC progression and in neurons and astrocytes. Additionally, we found that genes associated with neuropsychiatric disorders and brain cancer risk might play critical roles in the early telencephalic organizers and during NSC progression.
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Affiliation(s)
- Nicola Micali
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mingfeng Li
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Suel-Kee Kim
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Xoel Mato-Blanco
- Hospital del Mar Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia, Spain
| | | | - Jon I. Arellano
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Tianliuyun Gao
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mikihito Shibata
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kevin T. Gobeske
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Alvaro Duque
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Gabriel Santpere
- Hospital del Mar Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia, Spain
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Departments of Psychiatry, Genetics and Comparative Medicine, Wu Tsai Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Yale Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Pasko Rakic
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
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24
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Mohsin SN, Grezenko H, Khan S, Eshete FD, Shrestha S, Kamran M, Affaf M, Jama A, Gasim RW, Zubaer Ahmad D, Yadav I, Arif S, K C A, Khaliq AS. Bridging Development and Disruption: Comprehensive Insights into Focal Cortical Dysplasia and Epileptic Management. Cureus 2023; 15:e45996. [PMID: 37900524 PMCID: PMC10601976 DOI: 10.7759/cureus.45996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 10/31/2023] Open
Abstract
Focal cortical dysplasia (FCD) is a prominent neurological disorder characterized by disruptions in localized brain cell organization and development. This narrative review delineates the multi-faceted nature of FCD, emphasizing its correlation with drug-resistant epilepsy, predominantly in children and young adults. We explore the historical context of FCD, highlighting its indispensable role in shaping our comprehension of epilepsy and cortical anomalies. The clinical spectrum of FCD is broad, encompassing diverse seizure patterns, cognitive impairments, and associated neuropsychiatric disorders. We underscore the importance of differential diagnosis, with techniques ranging from electroencephalogram (EEG) interpretations to microscopic evaluations, and discuss advanced diagnostic modalities, such as the 3T magnetic resonance imaging (MRI) epilepsy protocols. Therapeutically, while anti-seizure medications are often first-line interventions, surgically refractory cases necessitate more invasive procedures, underscoring the importance of individualized treatment. Furthermore, the review touches upon the prognostic aspects of FCD, highlighting the importance of personalized care regimens, and provides insights into emerging therapeutic avenues, including the potential of the mammalian target of rapamycin (mTOR) pathway. Conclusively, this review accentuates the complex relationship between brain development and epileptogenicity inherent to FCD and underscores the promise of future research in enhancing patient outcomes.
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Affiliation(s)
| | - Han Grezenko
- Translational Neuroscience, Barrow Neurological Institute, Phoenix, USA
| | - Saadia Khan
- Community Medicine, Khyber Girls Medical College, Peshawar, PAK
| | | | - Shraddha Shrestha
- Internal Medicine, Nepal Korea Friendship Municipality Hospital, Bhaktapur, NPL
| | | | - Maryam Affaf
- Internal Medicine, Women's Medical and Dental College, Abbottabad, PAK
| | - Ayat Jama
- Internal Medicine, Nishtar Medical University, Multan, PAK
| | - Rayan W Gasim
- Internal Medicine, University of Khartoum, Khartoum, SDN
| | | | - Indresh Yadav
- Internal Medicine, Samar Hospital and Research Center Pvt. Ltd., Janakpur, NPL
- Internal Medicine, Community Based Medical College, Mymensingh, BGD
| | - Sidra Arif
- Urology, Jinnah Postgraduate Medical Center, Karachi, PAK
| | - Anil K C
- Medicine and Surgery, Patan Academy of Health Sciences, Kathmandu, NPL
- Internal Medicine and Neurology, California Institute of Behavioral Neurosciences & Psychology, California, USA
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25
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Du H, Pan B, Alund AW, Yan J, Chen Y, Robison TW, Chen T. Evaluation of mutagenic susceptibility of different stages in germ cell development of Caenorhabditis elegans using whole genome sequencing. Arch Toxicol 2023; 97:2261-2272. [PMID: 37209179 DOI: 10.1007/s00204-023-03526-z] [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: 03/20/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]
Abstract
In contrast to somatic mutations, mutations in germ cells affect every cell of any organism derived from the germ cell and therefore are related to numerous genetic diseases. However, there is no suitable assay to evaluate the mutagenic sensitivities of both male and female germ cells. The main type of Caenorhabditis elegans (C. elegans) is hermaphroditic, where spermatogenesis and oogenesis occur chronologically at specific stages, allowing induction of mutations in either sperm or eggs exclusively. In this study, we used the alkylating agent ethyl methanesulfonate and N-ethyl-N-nitrosourea to induce germline mutations in C. elegans at different developmental stages and analyzed mutation frequency and mutational spectrum from data gathered using next-generation sequencing (NGS) technology. Our results revealed low spontaneous mutation rates of C. elegans, along with distinct mutagenic effects elicited by the two mutagens. Our data show that the parental worms treated during germ cell mitosis, spermatogenesis, and oogenesis resulted in different mutation frequencies in their offspring, and female germ cells could be very susceptible to mutagen exposure during oogenesis. In summary, our study indicates that the use of C. elegans and its specific chronological hermaphroditism would be a promising way to explore the sensitivities of both male and female germ cells to mutagens.
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Affiliation(s)
- Hua Du
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China
| | - Bohu Pan
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Alexander W Alund
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
- Discovery Sciences | Medicine Design, Pfizer Inc., 280 Shennecossett Rd, Groton, CT, 06340, USA
| | - Jian Yan
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Ying Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Timothy W Robison
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA.
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26
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Boßelmann CM, Leu C, Lal D. Technological and computational approaches to detect somatic mosaicism in epilepsy. Neurobiol Dis 2023:106208. [PMID: 37343892 DOI: 10.1016/j.nbd.2023.106208] [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: 03/05/2023] [Revised: 06/03/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023] Open
Abstract
Lesional epilepsy is a common and severe disease commonly associated with malformations of cortical development, including focal cortical dysplasia and hemimegalencephaly. Recent advances in sequencing and variant calling technologies have identified several genetic causes, including both short/single nucleotide and structural somatic variation. In this review, we aim to provide a comprehensive overview of the methodological advancements in this field while highlighting the unresolved technological and computational challenges that persist, including ultra-low variant allele fractions in bulk tissue, low availability of paired control samples, spatial variability of mutational burden within the lesion, and the issue of false-positive calls and validation procedures. Information from genetic testing in focal epilepsy may be integrated into clinical care to inform histopathological diagnosis, postoperative prognosis, and candidate precision therapies.
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Affiliation(s)
- Christian M Boßelmann
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, London, UK.
| | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T., Cambridge, MA, USA; Cologne Center for Genomics (CCG), University of Cologne, Cologne, DE, USA
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27
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Yang X, Xu X, Breuss MW, Antaki D, Ball LL, Chung C, Shen J, Li C, George RD, Wang Y, Bae T, Cheng Y, Abyzov A, Wei L, Alexandrov LB, Sebat JL, Gleeson JG. Control-independent mosaic single nucleotide variant detection with DeepMosaic. Nat Biotechnol 2023; 41:870-877. [PMID: 36593400 PMCID: PMC10314968 DOI: 10.1038/s41587-022-01559-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 10/10/2022] [Indexed: 01/04/2023]
Abstract
Mosaic variants (MVs) reflect mutagenic processes during embryonic development and environmental exposure, accumulate with aging and underlie diseases such as cancer and autism. The detection of noncancer MVs has been computationally challenging due to the sparse representation of nonclonally expanded MVs. Here we present DeepMosaic, combining an image-based visualization module for single nucleotide MVs and a convolutional neural network-based classification module for control-independent MV detection. DeepMosaic was trained on 180,000 simulated or experimentally assessed MVs, and was benchmarked on 619,740 simulated MVs and 530 independent biologically tested MVs from 16 genomes and 181 exomes. DeepMosaic achieved higher accuracy compared with existing methods on biological data, with a sensitivity of 0.78, specificity of 0.83 and positive predictive value of 0.96 on noncancer whole-genome sequencing data, as well as doubling the validation rate over previous best-practice methods on noncancer whole-exome sequencing data (0.43 versus 0.18). DeepMosaic represents an accurate MV classifier for noncancer samples that can be implemented as an alternative or complement to existing methods.
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Affiliation(s)
- Xiaoxu Yang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
| | - Xin Xu
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Martin W Breuss
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Danny Antaki
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Laurel L Ball
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Changuk Chung
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Jiawei Shen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Chen Li
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Renee D George
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Yifan Wang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Yuhe Cheng
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Jonathan L Sebat
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
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Yang S, Kim SH, Kang M, Joo JY. Harnessing deep learning into hidden mutations of neurological disorders for therapeutic challenges. Arch Pharm Res 2023:10.1007/s12272-023-01450-5. [PMID: 37261600 DOI: 10.1007/s12272-023-01450-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/26/2023] [Indexed: 06/02/2023]
Abstract
The relevant study of transcriptome-wide variations and neurological disorders in the evolved field of genomic data science is on the rise. Deep learning has been highlighted utilizing algorithms on massive amounts of data in a human-like manner, and is expected to predict the dependency or druggability of hidden mutations within the genome. Enormous mutational variants in coding and noncoding transcripts have been discovered along the genome by far, despite of the fine-tuned genetic proofreading machinery. These variants could be capable of inducing various pathological conditions, including neurological disorders, which require lifelong care. Several limitations and questions emerge, including the use of conventional processes via limited patient-driven sequence acquisitions and decoding-based inferences as well as how rare variants can be deduced as a population-specific etiology. These puzzles require harnessing of advanced systems for precise disease prediction, drug development and drug applications. In this review, we summarize the pathophysiological discoveries of pathogenic variants in both coding and noncoding transcripts in neurological disorders, and the current advantage of deep learning applications. In addition, we discuss the challenges encountered and how to outperform them with advancing interpretation.
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Affiliation(s)
- Sumin Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Rm 407, Bldg.42, 55 Hanyangdaehak-Ro, Sangnok-Gu Ansan, Ansan, Gyeonggi-Do, 15588, Republic of Korea
| | - Sung-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Rm 407, Bldg.42, 55 Hanyangdaehak-Ro, Sangnok-Gu Ansan, Ansan, Gyeonggi-Do, 15588, Republic of Korea
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, NV, 89154, USA
| | - Jae-Yeol Joo
- Department of Pharmacy, College of Pharmacy, Hanyang University, Rm 407, Bldg.42, 55 Hanyangdaehak-Ro, Sangnok-Gu Ansan, Ansan, Gyeonggi-Do, 15588, Republic of Korea.
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Zhang M, Bouland GA, Holstege H, Reinders MJT. Identifying Aging and Alzheimer Disease-Associated Somatic Variations in Excitatory Neurons From the Human Frontal Cortex. Neurol Genet 2023; 9:e200066. [PMID: 37123987 PMCID: PMC10136684 DOI: 10.1212/nxg.0000000000200066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/03/2023] [Indexed: 05/02/2023]
Abstract
Background and Objectives With age, somatic mutations accumulated in human brain cells can lead to various neurologic disorders and brain tumors. Because the incidence rate of Alzheimer disease (AD) increases exponentially with age, investigating the association between AD and the accumulation of somatic mutation can help understand the etiology of AD. Methods We designed a somatic mutation detection workflow by contrasting genotypes derived from whole-genome sequencing (WGS) data with genotypes derived from scRNA-seq data and applied this workflow to 76 participants from the Religious Order Study and the Rush Memory and Aging Project (ROSMAP) cohort. We focused only on excitatory neurons, the dominant cell type in the scRNA-seq data. Results We identified 196 sites that harbored at least 1 individual with an excitatory neuron-specific somatic mutation (ENSM), and these 196 sites were mapped to 127 genes. The single base substitution (SBS) pattern of the putative ENSMs was best explained by signature SBS5 from the Catalogue of Somatic Mutations in Cancer (COSMIC) mutational signatures, a clock-like pattern correlating with the age of the individual. The count of ENSMs per individual also showed an increasing trend with age. Among the mutated sites, we found 2 sites tend to have more mutations in older individuals (16:6899517 [RBFOX1], p = 0.04; 4:21788463 [KCNIP4], p < 0.05). In addition, 2 sites were found to have a higher odds ratio to detect a somatic mutation in AD samples (6:73374221 [KCNQ5], p = 0.01 and 13:36667102 [DCLK1], p = 0.02). Thirty-two genes that harbor somatic mutations unique to AD and the KCNQ5 and DCLK1 genes were used for gene ontology (GO)-term enrichment analysis. We found the AD-specific ENSMs enriched in the GO-term "vocalization behavior" and "intraspecies interaction between organisms." Of interest we observed both age-specific and AD-specific ENSMs enriched in the K+ channel-associated genes. Discussion Our results show that combining scRNA-seq and WGS data can successfully detect putative somatic mutations. The putative somatic mutations detected from ROSMAP data set have provided new insights into the association of AD and aging with brain somatic mutagenesis.
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Affiliation(s)
- Meng Zhang
- Delft Bioinformatics Lab (M.Z., G.A.B., H.H., M.J.T.R.), Delft University of Technology; Department of Human Genetics (M.Z., H.H.), Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC; and Department of Human Genetics (G.A.B., M.J.T.R.), Leiden University Medical Center, the Netherlands
| | - Gerard A Bouland
- Delft Bioinformatics Lab (M.Z., G.A.B., H.H., M.J.T.R.), Delft University of Technology; Department of Human Genetics (M.Z., H.H.), Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC; and Department of Human Genetics (G.A.B., M.J.T.R.), Leiden University Medical Center, the Netherlands
| | - Henne Holstege
- Delft Bioinformatics Lab (M.Z., G.A.B., H.H., M.J.T.R.), Delft University of Technology; Department of Human Genetics (M.Z., H.H.), Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC; and Department of Human Genetics (G.A.B., M.J.T.R.), Leiden University Medical Center, the Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Lab (M.Z., G.A.B., H.H., M.J.T.R.), Delft University of Technology; Department of Human Genetics (M.Z., H.H.), Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC; and Department of Human Genetics (G.A.B., M.J.T.R.), Leiden University Medical Center, the Netherlands
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Metodiev D, Minkin K, Ruseva M, Ganeva R, Parvanov D, Nachev S. Pathomorphological Diagnostic Criteria for Focal Cortical Dysplasias and Other Common Epileptogenic Lesions—Review of the Literature. Diagnostics (Basel) 2023; 13:diagnostics13071311. [PMID: 37046529 PMCID: PMC10092959 DOI: 10.3390/diagnostics13071311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/20/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Focal cortical dysplasia (FCD) represents a heterogeneous group of morphological changes in the brain tissue that can predispose the development of pharmacoresistant epilepsy (recurring, unprovoked seizures which cannot be managed with medications). This group of neurological disorders affects not only the cerebral cortex but also the subjacent white matter. This work reviews the literature describing the morphological substrate of pharmacoresistant epilepsy. All illustrations presented in this study are obtained from brain biopsies from refractory epilepsy patients investigated by the authors. Regarding classification, there are three main FCD types, all of which involve cortical dyslamination. The 2022 revision of the International League Against Epilepsy (ILAE) FCD classification includes new histologically defined pathological entities: mild malformation of cortical development (mMCD), mild malformation of cortical development with oligodendroglial hyperplasia in frontal lobe epilepsy (MOGHE), and “no FCD on histopathology”. Although the pathomorphological characteristics of the various forms of focal cortical dysplasias are well known, their aetiologic and pathogenetic features remain elusive. The identification of genetic variants in FCD opens an avenue for novel treatment strategies, which are of particular utility in cases where total resection of the epileptogenic area is impossible.
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Autocatalytic base editing for RNA-responsive translational control. Nat Commun 2023; 14:1339. [PMID: 36906659 PMCID: PMC10008589 DOI: 10.1038/s41467-023-36851-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 02/20/2023] [Indexed: 03/13/2023] Open
Abstract
Genetic circuits that control transgene expression in response to pre-defined transcriptional cues would enable the development of smart therapeutics. To this end, here we engineer programmable single-transcript RNA sensors in which adenosine deaminases acting on RNA (ADARs) autocatalytically convert target hybridization into a translational output. Dubbed DART VADAR (Detection and Amplification of RNA Triggers via ADAR), our system amplifies the signal from editing by endogenous ADAR through a positive feedback loop. Amplification is mediated by the expression of a hyperactive, minimal ADAR variant and its recruitment to the edit site via an orthogonal RNA targeting mechanism. This topology confers high dynamic range, low background, minimal off-target effects, and a small genetic footprint. We leverage DART VADAR to detect single nucleotide polymorphisms and modulate translation in response to endogenous transcript levels in mammalian cells.
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Charalambous M, Fischer A, Potschka H, Walker MC, Raedt R, Vonck K, Boon P, Lohi H, Löscher W, Worrell G, Leeb T, McEvoy A, Striano P, Kluger G, Galanopoulou AS, Volk HA, Bhatti SFM. Translational veterinary epilepsy: A win-win situation for human and veterinary neurology. Vet J 2023; 293:105956. [PMID: 36791876 DOI: 10.1016/j.tvjl.2023.105956] [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: 03/22/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
Epilepsy is a challenging multifactorial disorder with a complex genetic background. Our current understanding of the pathophysiology and treatment of epilepsy has substantially increased due to animal model studies, including canine studies, but additional basic and clinical research is required. Drug-resistant epilepsy is an important problem in both dogs and humans, since seizure freedom is not achieved with the available antiseizure medications. The evaluation and exploration of pharmacological and particularly non-pharmacological therapeutic options need to remain a priority in epilepsy research. Combined efforts and sharing knowledge and expertise between human medical and veterinary neurologists are important for improving the treatment outcomes or even curing epilepsy in dogs. Such interactions could offer an exciting approach to translate the knowledge gained from people and rodents to dogs and vice versa. In this article, a panel of experts discusses the similarities and knowledge gaps in human and animal epileptology, with the aim of establishing a common framework and the basis for future translational epilepsy research.
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Affiliation(s)
- Marios Charalambous
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hannover, Hannover 30559, Germany.
| | - Andrea Fischer
- Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Munich 80539, Germany
| | - Heidrun Potschka
- Institute of Pharmacology, Toxicology and Pharmacy, Ludwig-Maximilians-University, Munich 80539, Germany
| | - Matthew C Walker
- Institute of Neurology, University College London, London WC1N 3JD, UK
| | - Robrecht Raedt
- Department of Neurology, 4brain, Ghent University, Ghent 9000, Belgium
| | - Kristl Vonck
- Department of Neurology, 4brain, Ghent University, Ghent 9000, Belgium
| | - Paul Boon
- Department of Neurology, 4brain, Ghent University, Ghent 9000, Belgium
| | - Hannes Lohi
- Department of Veterinary Biosciences, Department of Medical and Clinical Genetics, and Folkhälsan Research Center, University of Helsinki, Helsinki 00014, Finland
| | - Wolfgang Löscher
- Department of Pharmacology, Toxicology, and Pharmacy, University of Veterinary Medicine Hannover, Hannover 30559, Germany
| | | | - Tosso Leeb
- Institute of Genetics, University of Bern, Bern 3001, Switzerland
| | - Andrew McEvoy
- Institute of Neurology, University College London, London WC1N 3JD, UK
| | - Pasquale Striano
- IRCCS 'G. Gaslini', Genova 16147, Italy; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, Genova, Italy
| | - Gerhard Kluger
- Research Institute, Rehabilitation, Transition-Palliation', PMU Salzburg, Salzburg 5020, Austria; Clinic for Neuropediatrics and Neurorehabilitation, Epilepsy Center for Children and Adolescents, Schoen Clinic Vogtareuth, Vogtareuth 83569, Germany
| | - Aristea S Galanopoulou
- Saul R Korey Department of Neurology, Isabelle Rapin Division of Child Neurology, Dominick P. Purpura Department of Neuroscience, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Holger A Volk
- Department of Small Animal Medicine and Surgery, University of Veterinary Medicine Hannover, Hannover 30559, Germany
| | - Sofie F M Bhatti
- Faculty of Veterinary Medicine, Small Animal Department, Ghent University, Merelbeke 9820, Belgium
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D'Gama AM, Poduri A. Brain somatic mosaicism in epilepsy: Bringing results Back to the clinic. Neurobiol Dis 2023; 181:106104. [PMID: 36972791 DOI: 10.1016/j.nbd.2023.106104] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/28/2023] Open
Abstract
Over the past decade, there has been tremendous progress in understanding brain somatic mosaicism in epilepsy in the research setting. Access to resected brain tissue samples from patients with medically refractory epilepsy undergoing epilepsy surgery has been key to making these discoveries. In this review, we discuss the gap between making discoveries in the research setting and bringing results back to the clinical setting. Current clinical genetic testing mainly uses clinically accessible tissue samples, like blood and saliva, and can detect inherited and de novo germline variants and potentially non-brain-limited mosaic variants that have resulted from post-zygotic mutation (also called "somatic mutations"). Methods developed in the research setting to detect brain-limited mosaic variants using brain tissue samples need to be further translated and validated in the clinical setting, which will allow post-resection brain tissue genetic diagnoses. However, obtaining a genetic diagnosis after surgery for refractory focal epilepsy, when brain tissue samples are available, is arguably "too late" to guide precision management. Emerging methods using cerebrospinal fluid (CSF) and subdural electroencephalogram (SEEG) depth electrodes hold promise for establishing genetic diagnoses pre-resection without the need for actual brain tissue. In parallel, development of curation rules for interpreting the pathogenicity of mosaic variants, which have unique considerations compared to germline variants, will assist clinically accredited laboratories and epilepsy geneticists in making genetic diagnoses. Returning results of brain-limited mosaic variants to patients and their families will end their diagnostic odyssey and advance epilepsy precision management.
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Li Z, Min S, Alliey-Rodriguez N, Giase G, Cheng L, Craig DW, Faulkner GJ, Asif H, Liu C, Gershon ES. Single-neuron whole genome sequencing identifies increased somatic mutation burden in Alzheimer's disease related genes. Neurobiol Aging 2023; 123:222-232. [PMID: 36599749 DOI: 10.1016/j.neurobiolaging.2022.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/15/2022]
Abstract
Accumulation of somatic mutations in human neurons is associated with aging and neurodegeneration. To shed light on the somatic mutational burden in Alzheimer's disease (AD) neurons and get more insight into the role of somatic mutations in AD pathogenesis, we performed single-neuron whole genome sequencing to detect genome-wide somatic mutations (single nucleotide variants (SNVs) and Indels) in 96 single prefrontal cortex neurons from 8 AD patients and 8 elderly controls. We found that the mutational burden is ∼3000 somatic mutations per neuron genome in elderly subjects. AD patients have increased somatic mutation burden in AD-related annotation categories, including AD risk genes and differentially expressed genes in AD neurons. Mutational signature analysis showed somatic SNVs (sSNVs) primarily caused by aging and oxidative DNA damage processes but no significant difference was detected between AD and controls. Additionally, functional somatic mutations identified in AD patients showed significant enrichment in several AD-related pathways, including AD pathway, Notch-signaling pathway and Calcium-signaling pathway. These findings provide genetic insights into how somatic mutations may alter the function of single neurons and exert their potential roles in the pathogenesis of AD.
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Affiliation(s)
- Zongchang Li
- Department of Psychiatry, The Second Xiangya Hospital; Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China; Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL, USA
| | - Shishi Min
- Department of Psychiatry, The Second Xiangya Hospital; Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China; Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA; Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Ney Alliey-Rodriguez
- Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL, USA
| | - Gina Giase
- School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
| | - Lijun Cheng
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - David Wesley Craig
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, Woolloongabba, Queensland, Australia; Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Huma Asif
- Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL, USA.
| | - Chunyu Liu
- Department of Psychiatry, The Second Xiangya Hospital; Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China; Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, USA; School of Psychology, Shaanxi Normal University, Xi'an, China.
| | - Elliot S Gershon
- Department of Psychiatry and Behavioral Neurosciences, University of Chicago, Chicago, IL, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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The emergence of genotypic divergence and future precision medicine applications. HANDBOOK OF CLINICAL NEUROLOGY 2023; 192:87-99. [PMID: 36796950 DOI: 10.1016/b978-0-323-85538-9.00013-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Genotypic divergence is a term adapted from population genetics and intimately linked to evolution. We use divergence here to emphasize the differences that set individuals apart in any cohort. The history of genetics is filled with descriptions of genotypic differences, but causal inference of interindividual biological variation has been scarce. We suggest that the practice of precision medicine requires a divergent approach, an approach dependent on the causal interpretation of previous convergent (and preliminary) knowledge in the field. This knowledge has relied on convergent descriptive syndromology (lumping), which has overemphasized a reductionistic gene determinism on the quest of seeking associations without causal understanding. Regulatory variants with small effect and somatic mutations are some of the modifying factors that lead to incomplete penetrance and intrafamilial variable expressivity often observed in apparently monogenic clinical disorders. A truly divergent approach to precision medicine requires splitting, that is, the consideration of different layers of genetic phenomena that interact causally in a nonlinear fashion. This chapter reviews convergences and divergences in genetics and genomics, aiming to discuss what can be causally understood to approximate the as-yet utopian lands of Precision Medicine for patients with neurodegenerative disorders.
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Townsend SE, Westfall JJ, Navarro JB, Koboldt DC, Mardis ER, Miller KE, Bedrosian TA. Single-nuclei transcriptomics enable detection of somatic variants in patient brain tissue. Sci Rep 2023; 13:527. [PMID: 36631516 PMCID: PMC9834227 DOI: 10.1038/s41598-023-27700-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
Somatic variants are a major cause of human disease, including neurological disorders like focal epilepsies, but can be challenging to study due to their mosaicism in bulk tissue biopsies. Coupling single-cell genotype and transcriptomic data has potential to provide insight into the role somatic variants play in disease etiology, such as by determining what cell types are affected or how the mutations affect gene expression. Here, we asked whether commonly used single-nucleus 3'- or 5'-RNA-sequencing assays can be used to derive single-nucleus genotype data for a priori known variants that are located near to either end of a transcript. To that end, we compared performance of commercially available single-nuclei 3'- and 5'- gene expression kits using resected brain samples from three pediatric patients with focal epilepsy. We quantified the ability to detect genetic variants in single-nucleus datasets depending on distance from the transcript end. Finally, we demonstrated the ability to identify affected cell types in a patient with a RHEB somatic variant causing an epilepsy-associated cortical malformation. Our results demonstrate that single-nuclei 3' or 5'-RNA-sequencing data can be used to identify known somatic variants in single-nuclei when they are expressed within proximity to a transcript end.
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Affiliation(s)
- Sydney E. Townsend
- grid.240344.50000 0004 0392 3476Institute for Genomic Medicine, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215 USA ,grid.261331.40000 0001 2285 7943Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, OH 43210 USA
| | - Jesse J. Westfall
- grid.240344.50000 0004 0392 3476Institute for Genomic Medicine, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215 USA
| | - Jason B. Navarro
- grid.240344.50000 0004 0392 3476Institute for Genomic Medicine, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215 USA
| | - Daniel C. Koboldt
- grid.240344.50000 0004 0392 3476Institute for Genomic Medicine, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215 USA ,grid.261331.40000 0001 2285 7943Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43210 USA
| | - Elaine R. Mardis
- grid.240344.50000 0004 0392 3476Institute for Genomic Medicine, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215 USA ,grid.261331.40000 0001 2285 7943Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43210 USA ,grid.261331.40000 0001 2285 7943Department of Neurosurgery, College of Medicine, The Ohio State University, Columbus, OH 43210 USA
| | - Katherine E. Miller
- grid.240344.50000 0004 0392 3476Institute for Genomic Medicine, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215 USA ,grid.261331.40000 0001 2285 7943Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43210 USA
| | - Tracy A. Bedrosian
- grid.240344.50000 0004 0392 3476Institute for Genomic Medicine, The Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43215 USA ,grid.261331.40000 0001 2285 7943Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43210 USA
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Iourov IY, Gerasimov AP, Zelenova MA, Ivanova NE, Kurinnaia OS, Zabrodskaya YM, Demidova IA, Barantsevich ER, Vasin KS, Kolotii AD, Ushanov VV, Sitovskaya DA, Lobzhanidze TBA, Iuditskaia ME, Iakushev NS, Zhumatov MM, Vorsanova SG, Samochernyh KA. Cytogenomic epileptology. Mol Cytogenet 2023; 16:1. [PMID: 36600272 PMCID: PMC9814426 DOI: 10.1186/s13039-022-00634-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Molecular cytogenetic and cytogenomic studies have made a contribution to genetics of epilepsy. However, current genomic research of this devastative condition is generally focused on the molecular genetic aspects (i.e. gene hunting, detecting mutations in known epilepsy-associated genes, searching monogenic causes of epilepsy). Nonetheless, chromosomal abnormalities and copy number variants (CNVs) represent an important part of genetic defects causing epilepsy. Moreover, somatic chromosomal mosaicism and genome/chromosome instability seem to be a possible mechanism for a wide spectrum of epileptic conditions. This idea becomes even more attracting taking into account the potential of molecular neurocytogenetic (neurocytogenomic) studies of the epileptic brain. Unfortunately, analyses of chromosome numbers and structure in the affected brain or epileptogenic brain foci are rarely performed. Therefore, one may conclude that cytogenomic area of genomic epileptology is poorly researched. Accordingly, molecular cytogenetic and cytogenomic studies of the clinical cohorts and molecular neurocytogenetic analyses of the epileptic brain appear to be required. Here, we have performed a theoretical analysis to define the targets of the aforementioned studies and to highlight future directions for molecular cytogenetic and cytogenomic research of epileptic disorders in the widest sense. To succeed, we have formed a consortium, which is planned to perform at least a part of suggested research. Taking into account the nature of the communication, "cytogenomic epileptology" has been introduced to cover the research efforts in this field of medical genomics and epileptology. Additionally, initial results of studying cytogenomic variations in the Russian neurodevelopmental cohort are reviewed with special attention to epilepsy. In total, we have concluded that (i) epilepsy-associated cytogenomic variations require more profound research; (ii) ontological analyses of epilepsy genes affected by chromosomal rearrangements and/or CNVs with unraveling pathways implicating epilepsy-associated genes are beneficial for epileptology; (iii) molecular neurocytogenetic (neurocytogenomic) analysis of postoperative samples are warranted in patients suffering from epileptic disorders.
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Affiliation(s)
- Ivan Y. Iourov
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia ,grid.445984.00000 0001 2224 0652Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia
| | - Alexandr P. Gerasimov
- grid.452417.1Research Laboratory of Pediatric Neurosurgery, Polenov Neurosurgical Institute, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Maria A. Zelenova
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Natalya E. Ivanova
- grid.452417.1Scientific Department of Polenov Neurosurgical Institute, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Oksana S. Kurinnaia
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Yulia M. Zabrodskaya
- grid.452417.1Research Laboratory of Pathomorphology of the Nervous System, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Irina A. Demidova
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Evgeny R. Barantsevich
- grid.412460.5Postgraduate Neurology and Manual Medicine Department, Pavlov First Saint-Petersburg State Medical University, Saint Petersburg, Russia
| | - Kirill S. Vasin
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Alexey D. Kolotii
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Vseslav V. Ushanov
- grid.452417.1Department of Neurosurgery, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Darya A. Sitovskaya
- grid.452417.1Research Laboratory of Pathomorphology of the Nervous System, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Timur B.-A. Lobzhanidze
- grid.445931.e0000 0004 0471 4078Saint Petersburg State Pediatric Medical University, Saint Petersburg, Russia
| | - Maria E. Iuditskaia
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Nikita S. Iakushev
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Muslim M. Zhumatov
- grid.445931.e0000 0004 0471 4078Saint Petersburg State Pediatric Medical University, Saint Petersburg, Russia
| | - Svetlana G. Vorsanova
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Konstantin A. Samochernyh
- grid.452417.1Polenov Neurosurgical Institute, Almazov National Medical Research Centre, Saint Petersburg, Russia
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Yan Y, Zhang SC. Generation of Cerebral Cortical Neurons from Human Pluripotent Stem Cells in 3D Culture. Methods Mol Biol 2023; 2683:1-11. [PMID: 37300762 DOI: 10.1007/978-1-0716-3287-1_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] [Indexed: 06/12/2023]
Abstract
Human forebrain cortical neurons are essential for fundamental functions like memory and consciousness. Generation of cortical neurons from human pluripotent stem cells provides a great source for creating models specific to cortical neuron diseases and for developing therapeutics. This chapter describes a detailed and robust method for generating human mature cortical neurons from stem cells in 3D suspension culture.
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Affiliation(s)
- Yuanwei Yan
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Su-Chun Zhang
- Waisman Center, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA.
- Department of Neurology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA.
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Medical School, Singapore, Singapore.
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Wang X, Yu G, Yan Z, Wan L, Wang W, Cui L. Lung Cancer Subtype Diagnosis by Fusing Image-Genomics Data and Hybrid Deep Networks. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:512-523. [PMID: 34855599 DOI: 10.1109/tcbb.2021.3132292] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Accurate diagnosis of cancer subtypes is crucial for precise treatment, because different cancer subtypes are involved with different pathology and require different therapies. Although deep learning techniques have made great success in computer vision and other fields, they do not work well on Lung cancer subtype diagnosis, due to the distinction of slide images between different cancer subtypes is ambiguous. Furthermore, they often over-fit to high-dimensional genomics data with limited samples, and do not fuse the image and genomics data in a sensible way. In this paper, we propose a hybrid deep network based approach LungDIG for Lung cancer subtype Diagnosis by fusing Image-Genomics data. LungDIG first tiles the tissue slide image into small patches and extracts the patch-level features by fine-tuning an Inception-V3 model. Since the patches may contain some false positives in non-diagnostic regions, it further designs a patch-level feature combination strategy to integrate the extracted patch features and maintain the diversity between different cancer subtypes. At the same time, it extracts the genomics features from Copy Number Variation data by an attention based nonlinear extractor. Next, it fuses the image and genomics features by an attention based multilayer perceptron (MLP) to diagnose cancer subtype. Experiments on TCGA lung cancer data show that LungDIG can not only achieve higher accuracy for cancer subtype diagnosis than state-of-the-art methods, but also have a high authenticity and good interpretability.
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40
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Ralston NVC. Concomitant selenoenzyme inhibitor exposures as etiologic contributors to disease: Implications for preventative medicine. Arch Biochem Biophys 2023; 733:109469. [PMID: 36423662 DOI: 10.1016/j.abb.2022.109469] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022]
Abstract
The physiological activities of selenium (Se) occur through enzymes that incorporate selenocysteine (Sec), a rare but important amino acid. The human genome includes 25 genes coding for Sec that employ it to catalyze challenging reactions. Selenoenzymes control thyroid hormones, calcium activities, immune responses, and perform other vital roles, but most are devoted to preventing and reversing oxidative damage. As the most potent intracellular nucleophile (pKa 5.2), Sec is vulnerable to binding by metallic and organic soft electrophiles (E*). These electron poor reactants initially form covalent bonds with nucleophiles such as cysteine (Cys) whose thiol (pKa 8.3) forms adducts which function as suicide substrates for selenoenzymes. These adducts orient E* to interact with Sec and since Se has a higher affinity for E* than sulfur, the E* transfers to Sec and irreversibly inhibits the enzyme's activity. Organic electrophiles have lower Se-binding affinities than metallic E*, but exposure sources are more abundant. Individuals with poor Se status are more vulnerable to the toxic effects of high E* exposures. The relative E*:Se stoichiometries remain undefined, but the aggregate effects of multiple E* exposures are predicted to be additive and possibly synergistic under certain conditions. The potential for the combined Se-binding effects of common pharmaceutical, dietary, or environmental E* require study, but even temporary loss of selenoenzyme activities would accentuate oxidative damage to tissues. As various degenerative diseases are associated with accumulating DNA damage, defining the effects of complementary E* exposures on selenoenzyme activities may enhance the ability of preventative medicine to support healthy aging.
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Affiliation(s)
- Nicholas V C Ralston
- Earth System Science and Policy, University of North Dakota, Grand Forks, ND, USA.
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41
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Beopoulos A, Géa M, Fasano A, Iris F. RNA epitranscriptomics dysregulation: A major determinant for significantly increased risk of ASD pathogenesis. Front Neurosci 2023; 17:1101422. [PMID: 36875672 PMCID: PMC9978375 DOI: 10.3389/fnins.2023.1101422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Autism spectrum disorders (ASDs) are perhaps the most severe, intractable and challenging child psychiatric disorders. They are complex, pervasive and highly heterogeneous and depend on multifactorial neurodevelopmental conditions. Although the pathogenesis of autism remains unclear, it revolves around altered neurodevelopmental patterns and their implications for brain function, although these cannot be specifically linked to symptoms. While these affect neuronal migration and connectivity, little is known about the processes that lead to the disruption of specific laminar excitatory and inhibitory cortical circuits, a key feature of ASD. It is evident that ASD has multiple underlying causes and this multigenic condition has been considered to also dependent on epigenetic effects, although the exact nature of the factors that could be involved remains unclear. However, besides the possibility for differential epigenetic markings directly affecting the relative expression levels of individual genes or groups of genes, there are at least three mRNA epitranscriptomic mechanisms, which function cooperatively and could, in association with both genotypes and environmental conditions, alter spatiotemporal proteins expression patterns during brain development, at both quantitative and qualitative levels, in a tissue-specific, and context-dependent manner. As we have already postulated, sudden changes in environmental conditions, such as those conferred by maternal inflammation/immune activation, influence RNA epitranscriptomic mechanisms, with the combination of these processes altering fetal brain development. Herein, we explore the postulate whereby, in ASD pathogenesis, RNA epitranscriptomics might take precedence over epigenetic modifications. RNA epitranscriptomics affects real-time differential expression of receptor and channel proteins isoforms, playing a prominent role in central nervous system (CNS) development and functions, but also RNAi which, in turn, impact the spatiotemporal expression of receptors, channels and regulatory proteins irrespective of isoforms. Slight dysregulations in few early components of brain development, could, depending upon their extent, snowball into a huge variety of pathological cerebral alterations a few years after birth. This may very well explain the enormous genetic, neuropathological and symptomatic heterogeneities that are systematically associated with ASD and psychiatric disorders at large.
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Affiliation(s)
| | - Manuel Géa
- Bio-Modeling Systems, Tour CIT, Paris, France
| | - Alessio Fasano
- Division of Pediatric Gastroenterology and Nutrition, Mucosal Immunology and Biology Research Center, Center for Celiac Research and Treatment, Massachusetts General Hospital for Children, Boston, MA, United States
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Francis DI, Stark Z, Scheffer IE, Tan TY, Murali K, Gallacher L, Amor DJ, Goel H, Downie L, Stutterd CA, Krzesinski EI, Vasudevan A, Oertel R, Petrovic V, Boys A, Wei V, Burgess T, Dun K, Oliver KL, Baxter A, Hackett A, Ayres S, Lunke S, Kalitsis P, Wall M. Comparing saliva and blood for the detection of mosaic genomic abnormalities that cause syndromic intellectual disability. Eur J Hum Genet 2022; 31:521-525. [PMID: 36446895 PMCID: PMC10172398 DOI: 10.1038/s41431-022-01232-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/23/2022] [Accepted: 10/31/2022] [Indexed: 11/30/2022] Open
Abstract
AbstractWe aimed to determine whether SNP-microarray genomic testing of saliva had a greater diagnostic yield than blood for pathogenic copy number variants (CNVs). We selected patients who underwent CMA testing of both blood and saliva from 23,289 blood and 21,857 saliva samples. Our cohort comprised 370 individuals who had testing of both, 224 with syndromic intellectual disability (ID) and 146 with isolated ID. Mosaic pathogenic CNVs or aneuploidy were detected in saliva but not in blood in 20/370 (4.4%). All 20 individuals had syndromic ID, accounting for 9.1% of the syndromic ID sub-cohort. Pathogenic CNVs were large in size (median of 46 Mb), and terminal in nature, with median mosaicism of 27.5% (not exceeding 40%). By contrast, non-mosaic pathogenic CNVs were 100% concordant between blood and saliva, considerably smaller in size (median of 0.65 Mb), and predominantly interstitial in location. Given that salivary microarray testing has increased diagnostic utility over blood in individuals with syndromic ID, we recommend it as a first-tier testing in this group.
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de Barros MC, Silva AGB, Souza TGDS, Chagas CA, Machado JCB, Ferreira MRA, Soares LAL, Xavier VL, de Araújo LCC, Borba EFDO, da Silva TG, Alves RRDV, Coelho LCBB, de Oliveira AM, Napoleão TH, Paiva PMG. Evaluation of acute toxicity, 28-day repeated dose toxicity, and genotoxicity of Moringa oleifera leaves infusion and powder. JOURNAL OF ETHNOPHARMACOLOGY 2022; 296:115504. [PMID: 35760258 DOI: 10.1016/j.jep.2022.115504] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Moringa oleifera Lam. leaves infusion and powder are widely used by population due the nutritional and medicinal potentials, however data regarding safety of use are still inconclusive, leading to prohibition of this plant in some countries. AIM OF THE STUDY The present work investigated the nutritional and phytochemical composition, acute and 28-day repeated dose toxicity, and genotoxicity of M. oleifera leaves infusion and powder. MATERIALS AND METHODS For nutritional characterization of leaf powder, it was determined: humidity; mineral residue (ash); total lipid, protein, carbohydrate, and crude fiber contents; and total caloric value. Phytochemical composition was determined by high performance liquid chromatography (HPLC). The acute toxicity assay used Swiss female albino mice and oral administration in a single dose at 2000 and 5000 mg/kg of infusion or powder. The 28-day repeated dose toxicity assay employed female and male mice, with oral administration of infusion or powder at the doses 250, 500 and 1000 mg/kg. The animals were evaluated for body weight, water and feed consumption, biochemical and hematological parameters, and histology of the liver, spleen, and kidneys. In vivo genotoxicity and mutagenicity (2000 mg/kg) were evaluated by the comet assay and the micronucleus test, respectively. RESULTS Nutritional characterization confirmed that M. oleifera leaves are rich in proteins, carbohydrates, lipids, minerals, and fiber. HPLC indicated the presence of flavonoids and cinnamic derivatives as major polyphenols. Acute toxicity did not reveal alterations in weight gain and water and feed consumptions and no change in biochemical, hematological, and histological parameters. Behavior alterations was observed in the first 2 h after administration at 5000 mg/kg in both treatments. Infusion did not present toxicity when administered for 28 days. Conversely, the powder at 500 and 1000 mg/kg promoted liver and kidney damages observed through biochemical parameters and histopathology. Genotoxicity and mutagenicity were not detected at 2000 mg/kg. CONCLUSIONS The present study reveals that M. oleifera leaves are an important source of polyphenols and nutrients. Indiscriminate use of both infusion and crude leaf powder above 2000 mg/kg and powder at 500 and 1000 mg/kg are not recommended. Chronic toxicological studies and establishment of preparation protocols are suggested aiming to guarantee the safety in the use of M. oleifera leaves as nutraceutical by population.
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Affiliation(s)
| | | | | | - Cristiano Aparecido Chagas
- Centro Acadêmico de Vitória, Universidade Federal de Pernambuco, Vitória de Santo Antão, Pernambuco, Brazil.
| | - Janaína Carla Barbosa Machado
- Departamento de Farmácia, Centro de Ciências da Saúde, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil.
| | | | - Luiz Alberto Lira Soares
- Departamento de Farmácia, Centro de Ciências da Saúde, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil.
| | - Viviane Lansky Xavier
- Departamento de Nutrição, Centro Ciências da Saúde, Universidade Federal de Pernambuco, Cidade Universitária, Recife, Pernambuco, Brazil
| | - Larissa Cardoso Corrêa de Araújo
- Departamento de Antibióticos, Centro de Biociências, Universidade Federal de Pernambuco, Cidade Universitária, Recife, Pernambuco, Brazil.
| | | | - Teresinha Gonçalves da Silva
- Departamento de Antibióticos, Centro de Biociências, Universidade Federal de Pernambuco, Cidade Universitária, Recife, Pernambuco, Brazil.
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Luquette LJ, Miller MB, Zhou Z, Bohrson CL, Zhao Y, Jin H, Gulhan D, Ganz J, Bizzotto S, Kirkham S, Hochepied T, Libert C, Galor A, Kim J, Lodato MA, Garaycoechea JI, Gawad C, West J, Walsh CA, Park PJ. Single-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements. Nat Genet 2022; 54:1564-1571. [PMID: 36163278 PMCID: PMC9833626 DOI: 10.1038/s41588-022-01180-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 08/04/2022] [Indexed: 01/13/2023]
Abstract
Accurate somatic mutation detection from single-cell DNA sequencing is challenging due to amplification-related artifacts. To reduce this artifact burden, an improved amplification technique, primary template-directed amplification (PTA), was recently introduced. We analyzed whole-genome sequencing data from 52 PTA-amplified single neurons using SCAN2, a new genotyper we developed to leverage mutation signatures and allele balance in identifying somatic single-nucleotide variants (SNVs) and small insertions and deletions (indels) in PTA data. Our analysis confirms an increase in nonclonal somatic mutation in single neurons with age, but revises the estimated rate of this accumulation to 16 SNVs per year. We also identify artifacts in other amplification methods. Most importantly, we show that somatic indels increase by at least three per year per neuron and are enriched in functional regions of the genome such as enhancers and promoters. Our data suggest that indels in gene-regulatory elements have a considerable effect on genome integrity in human neurons.
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Affiliation(s)
- Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Michael B Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA
- Division of Neuropathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zinan Zhou
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Craig L Bohrson
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yifan Zhao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Doga Gulhan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Javier Ganz
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Samantha Kirkham
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Tino Hochepied
- Center for Inflammation Research, Flanders Institute for Biotechnolpogy (VIB), Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Claude Libert
- Center for Inflammation Research, Flanders Institute for Biotechnolpogy (VIB), Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Alon Galor
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Junho Kim
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Michael A Lodato
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Juan I Garaycoechea
- Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Charles Gawad
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
- Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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Mohiuddin M, Kooy RF, Pearson CE. De novo mutations, genetic mosaicism and human disease. Front Genet 2022; 13:983668. [PMID: 36226191 PMCID: PMC9550265 DOI: 10.3389/fgene.2022.983668] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Mosaicism—the existence of genetically distinct populations of cells in a particular organism—is an important cause of genetic disease. Mosaicism can appear as de novo DNA mutations, epigenetic alterations of DNA, and chromosomal abnormalities. Neurodevelopmental or neuropsychiatric diseases, including autism—often arise by de novo mutations that usually not present in either of the parents. De novo mutations might occur as early as in the parental germline, during embryonic, fetal development, and/or post-natally, through ageing and life. Mutation timing could lead to mutation burden of less than heterozygosity to approaching homozygosity. Developmental timing of somatic mutation attainment will affect the mutation load and distribution throughout the body. In this review, we discuss the timing of de novo mutations, spanning from mutations in the germ lineage (all ages), to post-zygotic, embryonic, fetal, and post-natal events, through aging to death. These factors can determine the tissue specific distribution and load of de novo mutations, which can affect disease. The disease threshold burden of somatic de novo mutations of a particular gene in any tissue will be important to define.
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Affiliation(s)
- Mohiuddin Mohiuddin
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Edegem, Belgium
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
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Ren P, Dong X, Vijg J. Age-related somatic mutation burden in human tissues. FRONTIERS IN AGING 2022; 3:1018119. [PMID: 36213345 PMCID: PMC9534562 DOI: 10.3389/fragi.2022.1018119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022]
Abstract
The genome of multicellular organisms carries the hereditary information necessary for the development of all organs and tissues and to maintain function in adulthood. To ensure the genetic stability of the species, genomes are protected against changes in sequence information. However, genomes are not static. De novo mutations in germline cells are passed on to offspring and generate the variation needed in evolution. Moreover, postzygotic mutations occur in all somatic cells during development and aging. These somatic mutations remain limited to the individual, generating tissues that are genome mosaics. Insight into such mutations and their consequences has been limited due to their extremely low abundance, with most mutations unique for each cell. Recent advances in sequencing, including whole genome sequencing at the single-cell level, have now led to the first insights into somatic mutation burdens in human tissues. Here, we will first briefly describe the latest methodology for somatic mutation analysis, then review our current knowledge of somatic mutation burden in human tissues and, finally, briefly discuss the possible functional impact of somatic mutations on the aging process and age-related diseases, including cancer and diseases other than cancer.
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Affiliation(s)
- Peijun Ren
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Peijun Ren, ; Xiao Dong, ; Jan Vijg, ,
| | - Xiao Dong
- Department of Genetics, Cell Biology and Development, Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, United States,*Correspondence: Peijun Ren, ; Xiao Dong, ; Jan Vijg, ,
| | - Jan Vijg
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Department of Genetics, Albert Einstein College of Medicine, New York City, NY, United States,*Correspondence: Peijun Ren, ; Xiao Dong, ; Jan Vijg, ,
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47
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Yıldız Bölükbaşı E, Karolak JA, Szafranski P, Gambin T, Willard N, Abman SH, Galambos C, Kinsella JP, Stankiewicz P. High-level gonosomal mosaicism for a pathogenic non-coding CNV deletion of the lung-specific FOXF1 enhancer in an unaffected mother of an infant with ACDMPV. Mol Genet Genomic Med 2022; 10:e2062. [PMID: 36124617 PMCID: PMC9651602 DOI: 10.1002/mgg3.2062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/22/2022] [Accepted: 09/08/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) results from haploinsufficiency of the mesenchymal transcription factor FOXF1 gene. To date, only one case of an ACDMPV-causative CNV deletion inherited from a very-low level somatic mosaic mother has been reported. METHODS Clinical, histopathological, and molecular studies, including whole genome sequencing, chromosomal microarray analysis, qPCR, and Sanger sequencing, followed by in vitro fertilization (IVF) with preimplantation genetic testing (PGT) were used to study a family with a deceased neonate with ACDMPV. RESULTS A pathogenic CNV deletion of the lung-specific FOXF1 enhancer in the proband was found to be inherited from an unaffected mother, 36% mosaic for this deletion in her peripheral blood cells. The qPCR analyses of saliva, buccal cells, urine, nail, and hair samples revealed 19%, 18%, 15%, 19%, and 27% variant allele fraction, respectively, indicating a high recurrence risk. Grandparental studies revealed that the deletion arose on the mother's paternal chromosome 16. PGT studies revealed 44% embryos with the deletion, reflecting high-level germline mosaicism. CONCLUSION Our data further demonstrate the importance of parental testing in ACDMPV families and reproductive usefulness of IVF with PGT in families with high-level parental gonosomal mosaicism.
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Affiliation(s)
| | - Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical MicrobiologyPoznan University of Medical SciencesPoznanPoland
| | | | - Tomasz Gambin
- Institute of Computer ScienceWarsaw University of TechnologyWarsawPoland
| | - Nicholas Willard
- Department of Pathology and Laboratory MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Steven H. Abman
- Department of PediatricsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Csaba Galambos
- Department of Pathology and Laboratory MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA,Department of PediatricsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - John P. Kinsella
- Department of PediatricsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Paweł Stankiewicz
- Department of Molecular & Human GeneticsBaylor College of MedicineHoustonTexasUSA
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48
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Xu W, Wu C, Peng Q, Lee J, Xia Y, Kawasaki S. Enhancing the diversity of self-replicating structures using active self-adapting mechanisms. Front Genet 2022; 13:958069. [PMID: 35957682 PMCID: PMC9360575 DOI: 10.3389/fgene.2022.958069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous varieties of life forms have filled the earth throughout evolution. Evolution consists of two processes: self-replication and interaction with the physical environment and other living things around it. Initiated by von Neumann et al. studies on self-replication in cellular automata have attracted much attention, which aim to explore the logical mechanism underlying the replication of living things. In nature, competition is a common and spontaneous resource to drive self-replications, whereas most cellular-automaton-based models merely focus on some self-protection mechanisms that may deprive the rights of other artificial life (loops) to live. Especially, Huang et al. designed a self-adaptive, self-replicating model using a greedy selection mechanism, which can increase the ability of loops to survive through an occasionally abandoning part of their own structural information, for the sake of adapting to the restricted environment. Though this passive adaptation can improve diversity, it is always limited by the loop’s original structure and is unable to evolve or mutate new genes in a way that is consistent with the adaptive evolution of natural life. Furthermore, it is essential to implement more complex self-adaptive evolutionary mechanisms not at the cost of increasing the complexity of cellular automata. To this end, this article proposes new self-adaptive mechanisms, which can change the information of structural genes and actively adapt to the environment when the arm of a self-replicating loop encounters obstacles, thereby increasing the chance of replication. Meanwhile, our mechanisms can also actively add a proper orientation to the current construction arm for the sake of breaking through the deadlock situation. Our new mechanisms enable active self-adaptations in comparison with the passive mechanism in the work of Huang et al. which is achieved by including a few rules without increasing the number of cell states as compared to the latter. Experiments demonstrate that this active self-adaptability can bring more diversity than the previous mechanism, whereby it may facilitate the emergence of various levels in self-replicating structures.
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Affiliation(s)
- Wenli Xu
- College of Computer Science, Chongqing University, Chongqing, China
| | - Chunrong Wu
- College of Computer Science, Chongqing University, Chongqing, China
- *Correspondence: Chunrong Wu,
| | - Qinglan Peng
- College of Computer Science, Chongqing University, Chongqing, China
| | - Jia Lee
- College of Computer Science, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Software Theory and Technology, Chongqing, China
| | - Yunni Xia
- College of Computer Science, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Software Theory and Technology, Chongqing, China
| | - Shuji Kawasaki
- Faculty of Science and Engineering, Iwate University, Morioka, Japan
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Epigenetic genes and epilepsy - emerging mechanisms and clinical applications. Nat Rev Neurol 2022; 18:530-543. [PMID: 35859062 DOI: 10.1038/s41582-022-00693-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2022] [Indexed: 12/21/2022]
Abstract
An increasing number of epilepsies are being attributed to variants in genes with epigenetic functions. The products of these genes include factors that regulate the structure and function of chromatin and the placing, reading and removal of epigenetic marks, as well as other epigenetic processes. In this Review, we provide an overview of the various epigenetic processes, structuring our discussion around five function-based categories: DNA methylation, histone modifications, histone-DNA crosstalk, non-coding RNAs and chromatin remodelling. We provide background information on each category, describing the general mechanism by which each process leads to altered gene expression. We also highlight key clinical and mechanistic aspects, providing examples of genes that strongly associate with epilepsy within each class. We consider the practical applications of these findings, including tissue-based and biofluid-based diagnostics and precision medicine-based treatments. We conclude that variants in epigenetic genes are increasingly found to be causally involved in the epilepsies, with implications for disease mechanisms, treatments and diagnostics.
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Manders F, van Boxtel R, Middelkamp S. The Dynamics of Somatic Mutagenesis During Life in Humans. FRONTIERS IN AGING 2022; 2:802407. [PMID: 35822044 PMCID: PMC9261377 DOI: 10.3389/fragi.2021.802407] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022]
Abstract
From conception to death, human cells accumulate somatic mutations in their genomes. These mutations can contribute to the development of cancer and non-malignant diseases and have also been associated with aging. Rapid technological developments in sequencing approaches in the last few years and their application to normal tissues have greatly advanced our knowledge about the accumulation of these mutations during healthy aging. Whole genome sequencing studies have revealed that there are significant differences in mutation burden and patterns across tissues, but also that the mutation rates within tissues are surprisingly constant during adult life. In contrast, recent lineage-tracing studies based on whole-genome sequencing have shown that the rate of mutation accumulation is strongly increased early in life before birth. These early mutations, which can be shared by many cells in the body, may have a large impact on development and the origin of somatic diseases. For example, cancer driver mutations can arise early in life, decades before the detection of the malignancy. Here, we review the recent insights in mutation accumulation and mutagenic processes in normal tissues. We compare mutagenesis early and later in life and discuss how mutation rates and patterns evolve during aging. Additionally, we outline the potential impact of these mutations on development, aging and disease.
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Affiliation(s)
- Freek Manders
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands
| | - Sjors Middelkamp
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands
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