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Sandran NG, Fornarino DL, Corbett MA, Kroes T, Gardner AE, MacLennan AH, Gécz J, van Eyk CL. Application of multiple mosaic callers improves post-zygotic mutation detection from exome sequencing data. Genet Med 2024; 26:101220. [PMID: 39041334 DOI: 10.1016/j.gim.2024.101220] [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: 11/21/2023] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024] Open
Abstract
PURPOSE The gold standard for identification of post-zygotic variants (PZVs) is droplet digital polymerase chain reaction or high-depth sequencing across multiple tissues types. These approaches are yet to be systematically implemented for monogenic disorders. We developed PZV detection pipelines for correct classification of de novo variants. METHOD Our pipelines detect PZV in parents (gonosomal mosaicism [pGoM]) and children (somatic mosaicism, "M3"). We applied them to research exome sequencing (ES) data from the Australian Cerebral Palsy Biobank (n = 145 trios) and Simons Simplex Collection (n = 405 families). Candidate mosaic variants were validated using deep amplicon sequencing or droplet digital polymerase chain reaction. RESULTS 69.2% (M3trio), 63.9% (M3single), and 92.7% (pGoM) of detected variants were validated, with 48.6%, 56.7%, and 26.2% of variants, respectively, meeting strict criteria for mosaicism. In the Australian Cerebral Palsy Biobank, 16.6% of probands and 20.7% of parents had at least 1 true-positive somatic or pGoM variant, respectively. A large proportion of PZVs detected in Simons Simplex Collection parents (79.8%) and child (94.5%) were not previously reported. We reclassified 3.7% to 8.0% of germline de novo variants as mosaic. CONCLUSION Many PZVs were incorrectly classified as germline variants or missed by previous approaches. Systematic application of our pipelines could increase genetic diagnostic rate, improve estimates of recurrence risk in families, and benefit novel disease gene identification.
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Affiliation(s)
- Nandini G Sandran
- Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Australian Collaborative Cerebral Palsy Research Group, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Dani L Fornarino
- Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Australian Collaborative Cerebral Palsy Research Group, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Mark A Corbett
- Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Australian Collaborative Cerebral Palsy Research Group, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Thessa Kroes
- Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Alison E Gardner
- Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia
| | - Alastair H MacLennan
- Australian Collaborative Cerebral Palsy Research Group, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Jozef Gécz
- Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Australian Collaborative Cerebral Palsy Research Group, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia.
| | - Clare L van Eyk
- Neurogenetics Research Program, Adelaide Medical School, University of Adelaide, Adelaide, SA, Australia; Australian Collaborative Cerebral Palsy Research Group, Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
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2
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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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3
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Lee AT, Chang EF, Paredes MF, Nowakowski TJ. Large-scale neurophysiology and single-cell profiling in human neuroscience. Nature 2024; 630:587-595. [PMID: 38898291 DOI: 10.1038/s41586-024-07405-0] [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: 07/06/2023] [Accepted: 04/09/2024] [Indexed: 06/21/2024]
Abstract
Advances in large-scale single-unit human neurophysiology, single-cell RNA sequencing, spatial transcriptomics and long-term ex vivo tissue culture of surgically resected human brain tissue have provided an unprecedented opportunity to study human neuroscience. In this Perspective, we describe the development of these paradigms, including Neuropixels and recent brain-cell atlas efforts, and discuss how their convergence will further investigations into the cellular underpinnings of network-level activity in the human brain. Specifically, we introduce a workflow in which functionally mapped samples of human brain tissue resected during awake brain surgery can be cultured ex vivo for multi-modal cellular and functional profiling. We then explore how advances in human neuroscience will affect clinical practice, and conclude by discussing societal and ethical implications to consider. Potential findings from the field of human neuroscience will be vast, ranging from insights into human neurodiversity and evolution to providing cell-type-specific access to study and manipulate diseased circuits in pathology. This Perspective aims to provide a unifying framework for the field of human neuroscience as we welcome an exciting era for understanding the functional cytoarchitecture of the human brain.
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Affiliation(s)
- Anthony T Lee
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Edward F Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Mercedes F Paredes
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Tomasz J Nowakowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA.
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
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4
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Sun C, Kathuria K, Emery SB, Kim B, Burbulis IE, Shin JH, Weinberger DR, Moran JV, Kidd JM, Mills RE, McConnell MJ. Mapping recurrent mosaic copy number variation in human neurons. Nat Commun 2024; 15:4220. [PMID: 38760338 PMCID: PMC11101435 DOI: 10.1038/s41467-024-48392-0] [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: 03/03/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
When somatic cells acquire complex karyotypes, they often are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development, but neurons are almost never the origin of brain cancers. Instead, somatic mutations in neurons can bring about neurodevelopmental disorders, and contribute to the polygenic landscape of neuropsychiatric and neurodegenerative disease. A subset of human neurons harbors idiosyncratic copy number variants (CNVs, "CNV neurons"), but previous analyses of CNV neurons are limited by relatively small sample sizes. Here, we develop an allele-based validation approach, SCOVAL, to corroborate or reject read-depth based CNV calls in single human neurons. We apply this approach to 2,125 frontal cortical neurons from a neurotypical human brain. SCOVAL identifies 226 CNV neurons, which include a subclass of 65 CNV neurons with highly aberrant karyotypes containing whole or substantial losses on multiple chromosomes. Moreover, we find that CNV location appears to be nonrandom. Recurrent regions of neuronal genome rearrangement contain fewer, but longer, genes.
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Affiliation(s)
- Chen Sun
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Kunal Kathuria
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI, 48109, USA
| | - ByungJun Kim
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Ian E Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, 22902, USA
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Sede de la Patagonia, Puerto Montt, Chile
| | - Joo Heon Shin
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD, 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences and Neuroscience, Johns Hopkins School of Medicine, 600 North Wolfe Street, Baltimore, MD, 21287, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 733 North Broadway, Baltimore, MD, 21230, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, 1500 East Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Jeffrey M Kidd
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI, 48109, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA.
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI, 48109, USA.
| | - Michael J McConnell
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD, 21205, USA.
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5
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Barbitoff YA, Ushakov MO, Lazareva TE, Nasykhova YA, Glotov AS, Predeus AV. Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges. Brief Bioinform 2024; 25:bbad508. [PMID: 38271481 PMCID: PMC10810331 DOI: 10.1093/bib/bbad508] [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: 08/09/2023] [Revised: 11/18/2023] [Accepted: 12/12/2023] [Indexed: 01/27/2024] Open
Abstract
Next-generation sequencing (NGS) has revolutionized the field of rare disease diagnostics. Whole exome and whole genome sequencing are now routinely used for diagnostic purposes; however, the overall diagnosis rate remains lower than expected. In this work, we review current approaches used for calling and interpretation of germline genetic variants in the human genome, and discuss the most important challenges that persist in the bioinformatic analysis of NGS data in medical genetics. We describe and attempt to quantitatively assess the remaining problems, such as the quality of the reference genome sequence, reproducible coverage biases, or variant calling accuracy in complex regions of the genome. We also discuss the prospects of switching to the complete human genome assembly or the human pan-genome and important caveats associated with such a switch. We touch on arguably the hardest problem of NGS data analysis for medical genomics, namely, the annotation of genetic variants and their subsequent interpretation. We highlight the most challenging aspects of annotation and prioritization of both coding and non-coding variants. Finally, we demonstrate the persistent prevalence of pathogenic variants in the coding genome, and outline research directions that may enhance the efficiency of NGS-based disease diagnostics.
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Affiliation(s)
- Yury A Barbitoff
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
- Bioinformatics Institute, Kentemirovskaya st. 2A, 197342, St. Petersburg, Russia
| | - Mikhail O Ushakov
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
| | - Tatyana E Lazareva
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
| | - Yulia A Nasykhova
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
| | - Andrey S Glotov
- Dpt. of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, Mendeleevskaya line 3, 199034, St. Petersburg, Russia
| | - Alexander V Predeus
- Bioinformatics Institute, Kentemirovskaya st. 2A, 197342, St. Petersburg, Russia
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6
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Ha YJ, Kang S, Kim J, Kim J, Jo SY, Kim S. Comprehensive benchmarking and guidelines of mosaic variant calling strategies. Nat Methods 2023; 20:2058-2067. [PMID: 37828153 PMCID: PMC10703685 DOI: 10.1038/s41592-023-02043-2] [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: 12/11/2022] [Accepted: 09/12/2023] [Indexed: 10/14/2023]
Abstract
Rapid advances in sequencing and analysis technologies have enabled the accurate detection of diverse forms of genomic variants represented as heterozygous, homozygous and mosaic mutations. However, the best practices for mosaic variant calling remain disorganized owing to the technical and conceptual difficulties faced in evaluation. Here we present our benchmark of 11 feasible mosaic variant detection approaches based on a systematically designed whole-exome-level reference standard that mimics mosaic samples, supported by 354,258 control positive mosaic single-nucleotide variants and insertion-deletion mutations and 33,111,725 control negatives. We identified not only the best practice for mosaic variant detection but also the condition-dependent strengths and weaknesses of the current methods. Furthermore, feature-level evaluation and their combinatorial usage across multiple algorithms direct the way for immediate to prolonged improvements in mosaic variant detection. Our results will guide researchers in selecting suitable calling algorithms and suggest future strategies for developers.
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Affiliation(s)
- Yoo-Jin Ha
- Translational Genome Informatics Laboratory, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seungseok Kang
- Translational Genome Informatics Laboratory, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jisoo Kim
- Translational Genome Informatics Laboratory, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Junhan Kim
- Translational Genome Informatics Laboratory, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Se-Young Jo
- Translational Genome Informatics Laboratory, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sangwoo Kim
- Translational Genome Informatics Laboratory, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea.
- POSTECH Biotechnology Center, Pohang University of Science and Technology, Pohang, Republic of Korea.
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7
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Garrison MA, Jang Y, Bae T, Cherskov A, Emery SB, Fasching L, Jones A, Moldovan JB, Molitor C, Pochareddy S, Peters MA, Shin JH, Wang Y, Yang X, Akbarian S, Chess A, Gage FH, Gleeson JG, Kidd JM, McConnell M, Mills RE, Moran JV, Park PJ, Sestan N, Urban AE, Vaccarino FM, Walsh CA, Weinberger DR, Wheelan SJ, Abyzov A. Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases. Sci Data 2023; 10:813. [PMID: 37985666 PMCID: PMC10662356 DOI: 10.1038/s41597-023-02645-7] [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: 04/27/2023] [Accepted: 10/16/2023] [Indexed: 11/22/2023] Open
Abstract
Somatic mosaicism is defined as an occurrence of two or more populations of cells having genomic sequences differing at given loci in an individual who is derived from a single zygote. It is a characteristic of multicellular organisms that plays a crucial role in normal development and disease. To study the nature and extent of somatic mosaicism in autism spectrum disorder, bipolar disorder, focal cortical dysplasia, schizophrenia, and Tourette syndrome, a multi-institutional consortium called the Brain Somatic Mosaicism Network (BSMN) was formed through the National Institute of Mental Health (NIMH). In addition to genomic data of affected and neurotypical brains, the BSMN also developed and validated a best practices somatic single nucleotide variant calling workflow through the analysis of reference brain tissue. These resources, which include >400 terabytes of data from 1087 subjects, are now available to the research community via the NIMH Data Archive (NDA) and are described here.
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Affiliation(s)
- McKinzie A Garrison
- Program in Biochemistry, Molecular and Cellular Biology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Yeongjun Jang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Adriana Cherskov
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Liana Fasching
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Attila Jones
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John B Moldovan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Cindy Molitor
- Sage Bionetworks, 2901 Third Ave., Suite 330, Seattle, WA, 98121, USA
| | - Sirisha Pochareddy
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Mette A Peters
- Sage Bionetworks, 2901 Third Ave., Suite 330, Seattle, WA, 98121, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Yifan Wang
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Xiaoxu Yang
- Rady Children's Institute for Genomic Medicine, 7910 Frost St., Suite #300, San Diego, CA, 92123, USA
- Department of Neurosciences, University of California San Diego, La Jolla, California, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technologies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Chess
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technologies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fred H Gage
- Laboratory of Genetics LOG-G, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, 7910 Frost St., Suite #300, San Diego, CA, 92123, USA
- Department of Neurosciences, University of California San Diego, La Jolla, California, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
| | | | - Ryan E Mills
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Flora M Vaccarino
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sarah J Wheelan
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- National Human Genome Research Institute, National Institutes of Health, 6700B Rockledge Dr, Bethesda, MD, 20892, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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8
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Lee HM, Hong SJ, Gill R, Caldairou B, Wang I, Zhang JG, Deleo F, Schrader D, Bartolomei F, Guye M, Cho KH, Barba C, Sisodiya S, Jackson G, Hogan RE, Wong-Kisiel L, Cascino GD, Schulze-Bonhage A, Lopes-Cendes I, Cendes F, Guerrini R, Bernhardt B, Bernasconi N, Bernasconi A. Multimodal mapping of regional brain vulnerability to focal cortical dysplasia. Brain 2023; 146:3404-3415. [PMID: 36852571 PMCID: PMC10393418 DOI: 10.1093/brain/awad060] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/17/2023] [Accepted: 02/02/2023] [Indexed: 03/01/2023] Open
Abstract
Focal cortical dysplasia (FCD) type II is a highly epileptogenic developmental malformation and a common cause of surgically treated drug-resistant epilepsy. While clinical observations suggest frequent occurrence in the frontal lobe, mechanisms for such propensity remain unexplored. Here, we hypothesized that cortex-wide spatial associations of FCD distribution with cortical cytoarchitecture, gene expression and organizational axes may offer complementary insights into processes that predispose given cortical regions to harbour FCD. We mapped the cortex-wide MRI distribution of FCDs in 337 patients collected from 13 sites worldwide. We then determined its associations with (i) cytoarchitectural features using histological atlases by Von Economo and Koskinas and BigBrain; (ii) whole-brain gene expression and spatiotemporal dynamics from prenatal to adulthood stages using the Allen Human Brain Atlas and PsychENCODE BrainSpan; and (iii) macroscale developmental axes of cortical organization. FCD lesions were preferentially located in the prefrontal and fronto-limbic cortices typified by low neuron density, large soma and thick grey matter. Transcriptomic associations with FCD distribution uncovered a prenatal component related to neuroglial proliferation and differentiation, likely accounting for the dysplastic makeup, and a postnatal component related to synaptogenesis and circuit organization, possibly contributing to circuit-level hyperexcitability. FCD distribution showed a strong association with the anterior region of the antero-posterior axis derived from heritability analysis of interregional structural covariance of cortical thickness, but not with structural and functional hierarchical axes. Reliability of all results was confirmed through resampling techniques. Multimodal associations with cytoarchitecture, gene expression and axes of cortical organization indicate that prenatal neurogenesis and postnatal synaptogenesis may be key points of developmental vulnerability of the frontal lobe to FCD. Concordant with a causal role of atypical neuroglial proliferation and growth, our results indicate that FCD-vulnerable cortices display properties indicative of earlier termination of neurogenesis and initiation of cell growth. They also suggest a potential contribution of aberrant postnatal synaptogenesis and circuit development to FCD epileptogenicity.
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Affiliation(s)
- Hyo M Lee
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Seok-Jun Hong
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute, McGill University, Montreal, Canada
- Center for Neuroscience Imaging, Research Institute for Basic Science, Department of Global Biomedical Engineering, SungKyunKwan University, Suwon, KoreaSuwon, Korea
| | - Ravnoor Gill
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Benoit Caldairou
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Irene Wang
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Jian-guo Zhang
- Department of Functional Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Francesco Deleo
- Epilepsy Unit, Fondazione IRCCS Istituto Neurologico C. Besta, Milano, Italy
| | - Dewi Schrader
- Department of Pediatrics, British Columbia Children’s Hospital, Vancouver, Canada
| | - Fabrice Bartolomei
- Aix Marseille Univ, INSERM, INS, Institut de Neurosciences des Systèmes, Marseille, 13005, France
| | - Maxime Guye
- Aix Marseille University, CNRS, CRMBM UMR 7339, Marseille, France
| | - Kyoo Ho Cho
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
| | - Carmen Barba
- Meyer Children's Hospital IRCCS, Florence, Italy
- University of Florence, 50121 Florence, Italy
| | - Sanjay Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
| | - Graeme Jackson
- The Florey Institute of Neuroscience and Mental Health and The University of Melbourne, Victoria, Australia
| | - R Edward Hogan
- Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | | | | | | | - Iscia Lopes-Cendes
- Department of Translational Medicine, School of Medical Sciences, University of Campinas (UNICAMP) and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas SP, Brazil
| | - Fernando Cendes
- Department of Neurology, School of Medical Sciences, University of Campinas (UNICAMP), and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas SP, Brazil
| | - Renzo Guerrini
- Meyer Children's Hospital IRCCS, Florence, Italy
- University of Florence, 50121 Florence, Italy
| | - Boris Bernhardt
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Neda Bernasconi
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Andrea Bernasconi
- Neuroimaging of Epilepsy Laboratory, Montreal Neurological Institute, McGill University, Montreal, Canada
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9
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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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10
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Bizzotto S. The human brain through the lens of somatic mosaicism. Front Neurosci 2023; 17:1172469. [PMID: 37250426 PMCID: PMC10213359 DOI: 10.3389/fnins.2023.1172469] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023] Open
Abstract
Every cell in the human brain possesses a unique genome that is the product of the accumulation of somatic mutations starting from the first postzygotic cell division and continuing throughout life. Somatic mosaicism in the human brain has been the focus of several recent efforts that took advantage of key technological innovations to start elucidating brain development, aging and disease directly in human tissue. On one side, somatic mutation occurring in progenitor cells has been used as a natural barcoding system to address cell phylogenies of clone formation and cell segregation in the brain lineage. On the other side, analyses of mutation rates and patterns in the genome of brain cells have revealed mechanisms of brain aging and disorder predisposition. In addition to the study of somatic mosaicism in the normal human brain, the contribution of somatic mutation has been investigated in both developmental neuropsychiatric and neurodegenerative disorders. This review starts with a methodological perspective on the study of somatic mosaicism to then cover the most recent findings in brain development and aging, and ends with the role of somatic mutations in brain disease. Thus, this review underlies what we have learned and what is still possible to discover by looking at somatic mosaicism in the brain genome.
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11
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Sun C, Kathuria K, Emery SB, Kim B, Burbulis IE, Shin JH, Weinberger DR, Moran JV, Kidd JM, Mills RE, McConnell MJ. Mapping the Complex Genetic Landscape of Human Neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531594. [PMID: 36945473 PMCID: PMC10028870 DOI: 10.1101/2023.03.07.531594] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
When somatic cells acquire complex karyotypes, they are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development, but neurons are almost never the origin of brain cancers. Instead, somatic mutations in neurons can bring about neurodevelopmental disorders, and contribute to the polygenic landscape of neuropsychiatric and neurodegenerative disease. A subset of human neurons harbors idiosyncratic copy number variants (CNVs, "CNV neurons"), but previous analyses of CNV neurons have been limited by relatively small sample sizes. Here, we developed an allele-based validation approach, SCOVAL, to corroborate or reject read-depth based CNV calls in single human neurons. We applied this approach to 2,125 frontal cortical neurons from a neurotypical human brain. This approach identified 226 CNV neurons, as well as a class of CNV neurons with complex karyotypes containing whole or substantial losses on multiple chromosomes. Moreover, we found that CNV location appears to be nonrandom. Recurrent regions of neuronal genome rearrangement contained fewer, but longer, genes.
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Affiliation(s)
- Chen Sun
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Kunal Kathuria
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - ByungJun Kim
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Ian E. Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA 22902, USA
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Sede de la Patagonia, Puerto Montt, Chile
| | - Joo Heon Shin
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | | | - Daniel R. Weinberger
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences and Neuroscience, Johns Hopkins School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 733 North Broadway, Baltimore, MD 21230, USA
| | - John V. Moran
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jeffrey M. Kidd
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Ryan E. Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Michael J. McConnell
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
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12
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Chung C, Yang X, Bae T, Vong KI, Mittal S, Donkels C, Westley Phillips H, Li Z, Marsh APL, Breuss MW, Ball LL, Garcia CAB, George RD, Gu J, Xu M, Barrows C, James KN, Stanley V, Nidhiry AS, Khoury S, Howe G, Riley E, Xu X, Copeland B, Wang Y, Kim SH, Kang HC, Schulze-Bonhage A, Haas CA, Urbach H, Prinz M, Limbrick DD, Gurnett CA, Smyth MD, Sattar S, Nespeca M, Gonda DD, Imai K, Takahashi Y, Chen HH, Tsai JW, Conti V, Guerrini R, Devinsky O, Silva WA, Machado HR, Mathern GW, Abyzov A, Baldassari S, Baulac S, Gleeson JG. Comprehensive multi-omic profiling of somatic mutations in malformations of cortical development. Nat Genet 2023; 55:209-220. [PMID: 36635388 PMCID: PMC9961399 DOI: 10.1038/s41588-022-01276-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 11/30/2022] [Indexed: 01/14/2023]
Abstract
Malformations of cortical development (MCD) are neurological conditions involving focal disruptions of cortical architecture and cellular organization that arise during embryogenesis, largely from somatic mosaic mutations, and cause intractable epilepsy. Identifying the genetic causes of MCD has been a challenge, as mutations remain at low allelic fractions in brain tissue resected to treat condition-related epilepsy. Here we report a genetic landscape from 283 brain resections, identifying 69 mutated genes through intensive profiling of somatic mutations, combining whole-exome and targeted-amplicon sequencing with functional validation including in utero electroporation of mice and single-nucleus RNA sequencing. Genotype-phenotype correlation analysis elucidated specific MCD gene sets associated with distinct pathophysiological and clinical phenotypes. The unique single-cell level spatiotemporal expression patterns of mutated genes in control and patient brains indicate critical roles in excitatory neurogenic pools during brain development and in promoting neuronal hyperexcitability after birth.
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Affiliation(s)
- 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
| | - 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
| | - Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Keng Ioi Vong
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Swapnil Mittal
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Catharina Donkels
- Department of Neurosurgery, Experimental Epilepsy Research, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - H Westley Phillips
- Department of Neurosurgery, University of California at Los Angeles, Los Angeles, CA, USA
| | - Zhen Li
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Ashley P L Marsh
- 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 Clinical Genetics and Metabolism, University of Colorado Aurora, Aurora, CO, 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
| | - Camila Araújo Bernardino Garcia
- Laboratory of Pediatric Neurosurgery and Developmental Neuropathology, Department of Surgery and Anatomy, University of São Paulo, Ribeirão Preto, Brazil
| | - 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
| | - Jing Gu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Mingchu Xu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Chelsea Barrows
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Kiely N James
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Anna S Nidhiry
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sami Khoury
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Gabrielle Howe
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Emily Riley
- 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
| | - Brett Copeland
- 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
| | - Se Hoon Kim
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Hoon-Chul Kang
- Division of Pediatric Neurology, Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Andreas Schulze-Bonhage
- Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carola A Haas
- Department of Neurosurgery, Experimental Epilepsy Research, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Horst Urbach
- Department of Neuroradiology, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Marco Prinz
- Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - David D Limbrick
- Department of Neurology, St. Louis Children's Hospital, Washington University St Louis, Washington, MO, USA
| | - Christina A Gurnett
- Department of Neurology, St. Louis Children's Hospital, Washington University St Louis, Washington, MO, USA
| | - Matthew D Smyth
- Department of Neurosurgery, St. Louis Children's Hospital, Washington University St Louis, Washington, MO, USA
| | - Shifteh Sattar
- Epilepsy Center, Rady Children's Hospital, San Diego, CA, USA
| | - Mark Nespeca
- Epilepsy Center, Rady Children's Hospital, San Diego, CA, USA
| | - David D Gonda
- Epilepsy Center, Rady Children's Hospital, San Diego, CA, USA
| | - Katsumi Imai
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Yukitoshi Takahashi
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Shizuoka, Japan
| | - Hsin-Hung Chen
- Division of Pediatric Neurosurgery, The Neurological Institute, Taipei Veterans General Hospital, Taipei City, Taiwan
| | - Jin-Wu Tsai
- Institute of Brain Science, Brain Research Center, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Valerio Conti
- Pediatric Neurology Unit and Laboratories, IRCCS Meyer Children's Hospital University of Florence, Firenze, Italy
| | - Renzo Guerrini
- Pediatric Neurology Unit and Laboratories, IRCCS Meyer Children's Hospital University of Florence, Firenze, Italy
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, Department of Neurology, New York University Langone Health, New York, NY, USA
| | - Wilson A Silva
- Department of Genetics, Center for Cell-Based Therapy, Center for Integrative Systems Biology, University of São Paulo, Ribeirão Preto, Brazil
| | - Helio R Machado
- Laboratory of Pediatric Neurosurgery and Developmental Neuropathology, Department of Surgery and Anatomy, University of São Paulo, Ribeirão Preto, Brazil
| | - Gary W Mathern
- Department of Neurosurgery, University of California at Los Angeles, Los Angeles, CA, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sara Baldassari
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Stéphanie Baulac
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpital de la Pitié Salpêtrière, Paris, France
| | - 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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13
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Grave-to-cradle: human embryonic lineage tracing from the postmortem body. Exp Mol Med 2023; 55:13-21. [PMID: 36599930 PMCID: PMC9898511 DOI: 10.1038/s12276-022-00912-y] [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: 04/04/2022] [Revised: 09/02/2022] [Accepted: 10/13/2022] [Indexed: 01/06/2023] Open
Abstract
Curiosity concerning the process of human creation has been around for a long time. Relevant questions seemed to be resolved with the knowledge of how cells divide after fertilization obtained through in vitro fertilization experiments. However, we still do not know how human life is created at the cellular level. Recently, the value of cadavers as a resource from which to obtain "normal" cells and tissues has been established, and human research using postmortem bodies has attracted growing scientific attention. As the human genome can be analyzed at the level of nucleotides through whole-genome sequencing, individual cells in a postmortem body can be traced back to determine what developmental processes have transpired from fertilization. These retrospective lineage tracing studies have answered several unsolved questions on how humans are created. This review covers the methodologies utilized in lineage tracing research in a historical context and the conceptual basis for reconstructing the division history of cells in a retrospective manner using postzygotic somatic variants in postmortem tissue. We further highlight answers that postmortem research could potentially address and discuss issues that wait to be solved in the future.
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14
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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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15
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Argouarch AR, Schultz N, Yang AC, Jang Y, Garcia K, Cosme CG, Corrales CI, Nana AL, Karydas AM, Spina S, Grinberg LT, Miller B, Wyss-Coray T, Abyzov A, Goodarzi H, Seeley WW, Kao AW. Postmortem Human Dura Mater Cells Exhibit Phenotypic, Transcriptomic and Genetic Abnormalities that Impact their Use for Disease Modeling. Stem Cell Rev Rep 2022; 18:3050-3065. [PMID: 35809166 PMCID: PMC9622518 DOI: 10.1007/s12015-022-10416-x] [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] [Accepted: 06/19/2022] [Indexed: 11/24/2022]
Abstract
Patient-derived cells hold great promise for precision medicine approaches in human health. Human dermal fibroblasts have been a major source of cells for reprogramming and differentiating into specific cell types for disease modeling. Postmortem human dura mater has been suggested as a primary source of fibroblasts for in vitro modeling of neurodegenerative diseases. Although fibroblast-like cells from human and mouse dura mater have been previously described, their utility for reprogramming and direct differentiation protocols has not been fully established. In this study, cells derived from postmortem dura mater are directly compared to those from dermal biopsies of living subjects. In two instances, we have isolated and compared dermal and dural cell lines from the same subject. Notably, striking differences were observed between cells of dermal and dural origin. Compared to dermal fibroblasts, postmortem dura mater-derived cells demonstrated different morphology, slower growth rates, and a higher rate of karyotype abnormality. Dura mater-derived cells also failed to express fibroblast protein markers. When dermal fibroblasts and dura mater-derived cells from the same subject were compared, they exhibited highly divergent gene expression profiles that suggest dura mater cells originated from a mixed mural lineage. Given their postmortem origin, somatic mutation signatures of dura mater-derived cells were assessed and suggest defective DNA damage repair. This study argues for rigorous karyotyping of postmortem derived cell lines and highlights limitations of postmortem human dura mater-derived cells for modeling normal biology or disease-associated pathobiology.
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Affiliation(s)
- Andrea R. Argouarch
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Nina Schultz
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Andrew C. Yang
- Department of Neurology and Neurological Sciences, School of Medicine, Stanford University, Stanford, CA 94304 USA
| | - Yeongjun Jang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Kristle Garcia
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158 USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Celica G. Cosme
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Christian I. Corrales
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Alissa L. Nana
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Anna M. Karydas
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Salvatore Spina
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Lea T. Grinberg
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
- Department of Pathology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Bruce Miller
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, School of Medicine, Stanford University, Stanford, CA 94304 USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158 USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94158 USA
| | - William W. Seeley
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
- Department of Pathology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Aimee W. Kao
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
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16
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Bae T, Fasching L, Wang Y, Shin JH, Suvakov M, Jang Y, Norton S, Dias C, Mariani J, Jourdon A, Wu F, Panda A, Pattni R, Chahine Y, Yeh R, Roberts RC, Huttner A, Kleinman JE, Hyde TM, Straub RE, Walsh CA, Urban AE, Leckman JF, Weinberger DR, Vaccarino FM, Abyzov A. Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability. Science 2022; 377:511-517. [PMID: 35901164 PMCID: PMC9420557 DOI: 10.1126/science.abm6222] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We analyzed 131 human brains (44 neurotypical, 19 with Tourette syndrome, 9 with schizophrenia, and 59 with autism) for somatic mutations after whole genome sequencing to a depth of more than 200×. Typically, brains had 20 to 60 detectable single-nucleotide mutations, but ~6% of brains harbored hundreds of somatic mutations. Hypermutability was associated with age and damaging mutations in genes implicated in cancers and, in some brains, reflected in vivo clonal expansions. Somatic duplications, likely arising during development, were found in ~5% of normal and diseased brains, reflecting background mutagenesis. Brains with autism were associated with mutations creating putative transcription factor binding motifs in enhancer-like regions in the developing brain. The top-ranked affected motifs corresponded to MEIS (myeloid ectopic viral integration site) transcription factors, suggesting a potential link between their involvement in gene regulation and autism.
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Affiliation(s)
- Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Liana Fasching
- Child Study Center, Yale University, New Haven, CT 06520
| | - Yifan Wang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Milovan Suvakov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Yeongjun Jang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Scott Norton
- Child Study Center, Yale University, New Haven, CT 06520
| | - Caroline Dias
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | | | | | - Feinan Wu
- Child Study Center, Yale University, New Haven, CT 06520
| | - Arijit Panda
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Yasmine Chahine
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Rebecca Yeh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Rosalinda C. Roberts
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham Al, 35294
| | - Anita Huttner
- Department of Pathology, Yale University, New Haven, CT 06520
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Richard E. Straub
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
| | - Christopher A. Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | | | - Alexander E. Urban
- Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | | | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD
| | - Flora M. Vaccarino
- Child Study Center, Yale University, New Haven, CT 06520
- Department of Neuroscience, Yale University, New Haven, CT 06520
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905
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17
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Wasilewska K, Gambin T, Rydzanicz M, Szczałuba K, Płoski R. Postzygotic mutations and where to find them - Recent advances and future implications in the field of non-neoplastic somatic mosaicism. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108426. [PMID: 35690331 DOI: 10.1016/j.mrrev.2022.108426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/05/2022] [Accepted: 06/03/2022] [Indexed: 01/01/2023]
Abstract
The technological progress of massively parallel sequencing (MPS) has triggered a remarkable development in the research on postzygotic mutations. Although the overwhelming majority of studies in the field focus on oncogenesis, non-neoplastic diseases are attracting more and more attention. The aim of this review was to summarize some of the most recent findings in the field of somatic mosaicism in diseases other than neoplastic events. We discuss the abundance and role of postzygotic mutations, with a special emphasis on disorders which occur only in a mosaic form (obligatory mosaic diseases; OMDs). Based on the list of OMDs compiled from the published literature and three databases (OMIM, Orphanet and MosaicBase), we demonstrate the prevalence of cancer-related genes across OMDs and suggest other sources to further explore OMDs and OMD-related genes. Additionally, we comment on some practical aspects related to mosaic diseases, such as approaches to tissue sampling, the MPS coverage required to detect variants at a very low frequency, as well as on bioinformatic and molecular tools dedicated to detect somatic mutations in MPS data.
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Affiliation(s)
- Krystyna Wasilewska
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Krzysztof Szczałuba
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, ul. Pawińskiego 3c, 02-106 Warsaw, Poland.
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18
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Lobon I, Solís-Moruno M, Juan D, Muhaisen A, Abascal F, Esteller-Cucala P, García-Pérez R, Martí MJ, Tolosa E, Ávila J, Rahbari R, Marques-Bonet T, Casals F, Soriano E. Somatic Mutations Detected in Parkinson Disease Could Affect Genes With a Role in Synaptic and Neuronal Processes. FRONTIERS IN AGING 2022; 3:851039. [PMID: 35821807 PMCID: PMC9261316 DOI: 10.3389/fragi.2022.851039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/16/2022] [Indexed: 12/17/2022]
Abstract
The role of somatic mutations in complex diseases, including neurodevelopmental and neurodegenerative disorders, is becoming increasingly clear. However, to date, no study has shown their relation to Parkinson disease’s phenotype. To explore the relevance of embryonic somatic mutations in sporadic Parkinson disease, we performed whole-exome sequencing in blood and four brain regions of ten patients. We identified 59 candidate somatic single nucleotide variants (sSNVs) through sensitive calling and a careful filtering strategy (COSMOS). We validated 27 of them with amplicon-based ultra-deep sequencing, with a 70% validation rate for the highest-confidence variants. The identified sSNVs are in genes with synaptic functions that are co-expressed with genes previously associated with Parkinson disease. Most of the sSNVs were only called in blood but were also found in the brain tissues with ultra-deep amplicon sequencing, demonstrating the strength of multi-tissue sampling designs.
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Affiliation(s)
- Irene Lobon
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
- *Correspondence: Irene Lobon, ; Eduardo Soriano,
| | - Manuel Solís-Moruno
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
| | - Ashraf Muhaisen
- Department of Cell Biology, Physiology and Immunology and Institute of Neurosciences, Universitat de Barcelona (UB), Barcelona, Spain
- Centre for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Federico Abascal
- Cancer, Ageing, and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, United Kingdom
| | | | | | - Maria Josep Martí
- Centre for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- Department of Neurology, Hospital Clínic de Barcelona, Institut d’Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Barcelona, Spain
| | - Eduardo Tolosa
- Centre for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- Department of Neurology, Hospital Clínic de Barcelona, Institut d’Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), University of Barcelona (UB), Barcelona, Spain
| | - Jesús Ávila
- Centre for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, Madrid, Spain
| | - Raheleh Rahbari
- Cancer, Ageing, and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ferran Casals
- Genomics Core Facility, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Eduardo Soriano
- Department of Cell Biology, Physiology and Immunology and Institute of Neurosciences, Universitat de Barcelona (UB), Barcelona, Spain
- Centre for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
- *Correspondence: Irene Lobon, ; Eduardo Soriano,
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19
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Breuss MW, Yang X, Schlachetzki JCM, Antaki D, Lana AJ, Xu X, Chung C, Chai G, Stanley V, Song Q, Newmeyer TF, Nguyen A, O'Brien S, Hoeksema MA, Cao B, Nott A, McEvoy-Venneri J, Pasillas MP, Barton ST, Copeland BR, Nahas S, Van Der Kraan L, Ding Y, Glass CK, Gleeson JG. Somatic mosaicism reveals clonal distributions of neocortical development. Nature 2022; 604:689-696. [PMID: 35444276 PMCID: PMC9436791 DOI: 10.1038/s41586-022-04602-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 02/25/2022] [Indexed: 11/09/2022]
Abstract
The structure of the human neocortex underlies species-specific traits and reflects intricate developmental programs. Here we sought to reconstruct processes that occur during early development by sampling adult human tissues. We analysed neocortical clones in a post-mortem human brain through a comprehensive assessment of brain somatic mosaicism, acting as neutral lineage recorders1,2. We combined the sampling of 25 distinct anatomic locations with deep whole-genome sequencing in a neurotypical deceased individual and confirmed results with 5 samples collected from each of three additional donors. We identified 259 bona fide mosaic variants from the index case, then deconvolved distinct geographical, cell-type and clade organizations across the brain and other organs. We found that clones derived after the accumulation of 90-200 progenitors in the cerebral cortex tended to respect the midline axis, well before the anterior-posterior or ventral-dorsal axes, representing a secondary hierarchy following the overall patterning of forebrain and hindbrain domains. Clones across neocortically derived cells were consistent with a dual origin from both dorsal and ventral cellular populations, similar to rodents, whereas the microglia lineage appeared distinct from other resident brain cells. Our data provide a comprehensive analysis of brain somatic mosaicism across the neocortex and demonstrate cellular origins and progenitor distribution patterns within the human brain.
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Affiliation(s)
- 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 Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - 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
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 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
| | - Addison J Lana
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, 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
| | - 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
| | - Guoliang Chai
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Qiong Song
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Traci F Newmeyer
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - An Nguyen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sydney O'Brien
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Marten A Hoeksema
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Beibei Cao
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Alexi Nott
- Department of Brain Sciences, Imperial College London, White City Campus, London, UK
- UK Dementia Research Institute, Imperial College London, White City Campus, London, UK
| | - Jennifer McEvoy-Venneri
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Martina P Pasillas
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Scott T Barton
- Division of Medical Education, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Brett R Copeland
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, 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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20
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Genetic mosaicism in the human brain: from lineage tracing to neuropsychiatric disorders. Nat Rev Neurosci 2022; 23:275-286. [PMID: 35322263 DOI: 10.1038/s41583-022-00572-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2022] [Indexed: 12/18/2022]
Abstract
Genetic mosaicism is the result of the accumulation of somatic mutations in the human genome starting from the first postzygotic cell generation and continuing throughout the whole life of an individual. The rapid development of next-generation and single-cell sequencing technologies is now allowing the study of genetic mosaicism in normal tissues, revealing unprecedented insights into their clonal architecture and physiology. The somatic variant repertoire of an adult human neuron is the result of somatic mutations that accumulate in the brain by different mechanisms and at different rates during development and ageing. Non-pathogenic developmental mutations function as natural barcodes that once identified in deep bulk or single-cell sequencing can be used to retrospectively reconstruct human lineages. This approach has revealed novel insights into the clonal structure of the human brain, which is a mosaic of clones traceable to the early embryo that contribute differentially to the brain and distinct areas of the cortex. Some of the mutations happening during development, however, have a pathogenic effect and can contribute to some epileptic malformations of cortical development and autism spectrum disorder. In this Review, we discuss recent findings in the context of genetic mosaicism and their implications for brain development and disease.
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21
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Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology. Genes (Basel) 2022; 13:genes13020333. [PMID: 35205378 PMCID: PMC8871714 DOI: 10.3390/genes13020333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
During the last decade, genetic testing has emerged as an important etiological diagnostic tool for Mendelian diseases, including pediatric neurological conditions. A genetic diagnosis has a considerable impact on disease management and treatment; however, many cases remain undiagnosed after applying standard diagnostic sequencing techniques. This review discusses various methods to improve the molecular diagnostic rates in these genomic cold cases. We discuss extended analysis methods to consider, non-Mendelian inheritance models, mosaicism, dual/multiple diagnoses, periodic re-analysis, artificial intelligence tools, and deep phenotyping, in addition to integrating various omics methods to improve variant prioritization. Last, novel genomic technologies, including long-read sequencing, artificial long-read sequencing, and optical genome mapping are discussed. In conclusion, a more comprehensive molecular analysis and a timely re-analysis of unsolved cases are imperative to improve diagnostic rates. In addition, our current understanding of the human genome is still limited due to restrictions in technologies. Novel technologies are now available that improve upon some of these limitations and can capture all human genomic variation more accurately. Last, we recommend a more routine implementation of high molecular weight DNA extraction methods that is coherent with the ability to use and/or optimally benefit from these novel genomic methods.
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22
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Deb BK, Bateup HS. Modeling Somatic Mutations Associated With Neurodevelopmental Disorders in Human Brain Organoids. Front Mol Neurosci 2022; 14:787243. [PMID: 35058746 PMCID: PMC8764387 DOI: 10.3389/fnmol.2021.787243] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are a collection of diseases with early life onset that often present with developmental delay, cognitive deficits, and behavioral conditions. In some cases, severe outcomes such as brain malformations and intractable epilepsy can occur. The mutations underlying NDDs may be inherited or de novo, can be gain- or loss-of-function, and can affect one or more genes. Recent evidence indicates that brain somatic mutations contribute to several NDDs, in particular malformations of cortical development. While advances in sequencing technologies have enabled the detection of these somatic mutations, the mechanisms by which they alter brain development and function are not well understood due to limited model systems that recapitulate these events. Human brain organoids have emerged as powerful models to study the early developmental events of the human brain. Brain organoids capture the developmental progression of the human brain and contain human-enriched progenitor cell types. Advances in human stem cell and genome engineering provide an opportunity to model NDD-associated somatic mutations in brain organoids. These organoids can be tracked throughout development to understand the impact of somatic mutations on early human brain development and function. In this review, we discuss recent evidence that somatic mutations occur in the developing human brain, that they can lead to NDDs, and discuss how they could be modeled using human brain organoids.
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Affiliation(s)
- Bipan K. Deb
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Helen S. Bateup
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
- *Correspondence: Helen S. Bateup
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23
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Somatic Mosaicism and Autism Spectrum Disorder. Genes (Basel) 2021; 12:genes12111699. [PMID: 34828306 PMCID: PMC8619103 DOI: 10.3390/genes12111699] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/23/2021] [Accepted: 10/23/2021] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a genetically heterogenous neurodevelopmental disorder. In the early years of next-generation sequencing, de novo germline variants were shown to contribute to ASD risk. These germline mutations are present in all of the cells of an affected individual and can be detected in any tissue, including clinically accessible DNA sources such as blood or saliva. In recent years, studies have also implicated de novo somatic variants in ASD risk. These somatic mutations arise postzygotically and are present in only a subset of the cells of an affected individual. Depending on the developmental time and progenitor cell in which a somatic mutation occurs, it may be detectable in some tissues and not in others. Somatic mutations detectable at relatively low sequencing coverage in clinically accessible tissues are suggested to contribute to 3-5% of simplex ASD diagnoses, and "brain limited" somatic mutations have been identified in postmortem ASD brain tissue. Somatic mutations likely represent the genetic diagnosis in a proportion of otherwise unexplained individuals with ASD, and brain limited somatic mutations can be used as markers to discover risk genes, cell types, brain regions, and cellular pathways important for ASD pathogenesis and to potentially target for therapeutics.
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24
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Yang X, Breuss MW, Xu X, Antaki D, James KN, Stanley V, Ball LL, George RD, Wirth SA, Cao B, Nguyen A, McEvoy-Venneri J, Chai G, Nahas S, Van Der Kraan L, Ding Y, Sebat J, Gleeson JG. Developmental and temporal characteristics of clonal sperm mosaicism. Cell 2021; 184:4772-4783.e15. [PMID: 34388390 PMCID: PMC8496133 DOI: 10.1016/j.cell.2021.07.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/12/2021] [Accepted: 07/14/2021] [Indexed: 01/07/2023]
Abstract
Throughout development and aging, human cells accumulate mutations resulting in genomic mosaicism and genetic diversity at the cellular level. Mosaic mutations present in the gonads can affect both the individual and the offspring and subsequent generations. Here, we explore patterns and temporal stability of clonal mosaic mutations in male gonads by sequencing ejaculated sperm. Through 300× whole-genome sequencing of blood and sperm from healthy men, we find each ejaculate carries on average 33.3 ± 12.1 (mean ± SD) clonal mosaic variants, nearly all of which are detected in serial sampling, with the majority absent from sampled somal tissues. Their temporal stability and mutational signature suggest origins during embryonic development from a largely immutable stem cell niche. Clonal mosaicism likely contributes a transmissible, predicted pathogenic exonic variant for 1 in 15 men, representing a life-long threat of transmission for these individuals and a significant burden on human population health.
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Affiliation(s)
- Xiaoxu Yang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Martin W Breuss
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Xin Xu
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Danny Antaki
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kiely N James
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Laurel L Ball
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Renee D George
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Sara A Wirth
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Beibei Cao
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - An Nguyen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Jennifer McEvoy-Venneri
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Guoliang Chai
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Shareef Nahas
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | | | - Yan Ding
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Jonathan Sebat
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA 92093, USA; Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA.
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