Abstract
Somatic mosaicism is a known cause of neurological disorders, including developmental brain malformations and epilepsy. Brain mosaicism is traditionally attributed to post-zygotic genetic alterations arising in fetal development. Here we describe post-zygotic rescue of meiotic errors as an alternate origin of brain mosaicism in patients with focal epilepsy who have mosaic chromosome 1q copy number gains. Genomic analysis showed evidence of an extra parentally derived chromosome 1q allele in the resected brain tissue from five of six patients. This copy number gain is observed only in patient brain tissue, but not in blood or buccal cells, and is strongly enriched in astrocytes. Astrocytes carrying chromosome 1q gains exhibit distinct gene expression signatures and hyaline inclusions, supporting a novel genetic association for astrocytic inclusions in epilepsy. Further, these data demonstrate an alternate mechanism of brain chromosomal mosaicism, with parentally derived copy number gain isolated to brain, reflecting rescue in other tissues during development.
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Data availability
The single-nuclei RNA-seq data presented in this publication has been deposited in NCBI Gene Expression Omnibus and is accessible through GEO Series accession number GSE221849. Exome sequencing data are available either through dbGAP (phs002128.v1.p1) or BioProject (PRJNA1017875). Capture and targeted sequencing results are available as supplementary data. Exome sequence data from 342 controls were obtained from the North American Brain Expression Consortium (NABEC—dbGAP Study Accession: phs001300.v1.p1), and 15 whole genome-sequenced controls available from the Brain Somatic Mosaicism Network (National Institute of Mental Health Data Archive). Human reference genome build GRCh38.p12 is available from Index of /genomes/all/GCF/000/001/405/GCF_000001405.26_GRCh38 (https://www.nih.gov/). The Allen Brain Map Human M1 Cortex Dataset is available from https://portal.brain-map.org/atlases-and-data/rnaseq/human-m1-10x.
Code availability
R scripts to analyze the data and generate the figures are available on GitHub (https://github.com/bedrosian-lab/1q_mosaicism).
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Acknowledgements
We thank the patients and families for contributing their specimens to advance our understanding of the genetic bases of epilepsy-associated brain malformations. We also thank R. K. Wilson and the Genomic Services Laboratory and Computational Genomics Group at Nationwide Children’s Hospital. The work was funded by the Nationwide Innovation Fund, L. B. Research and Education Foundation (N.S.), The Ohio State University Medical Scientist Training Program—T32 Training Grant—T32GM139784 (N.S.), NIH-NINDS (R01NS094596) to E.L.H., and NIH-NINDS (R01NS129784) to T.A.B. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. Some figures were created in BioRender. Data and/or research tools used in the preparation of this manuscript were obtained from the National Institute of Mental Health Data Archive. National Institute of Mental Health Data Archive is a collaborative informatics system created by the National Institutes of Health to provide a national resource to support and accelerate research in mental health. Dataset identifier(s): 2962. This manuscript reflects the views of the authors and may not reflect the opinions or views of the NIH or of the Submitters submitting original data to the National Institute of Mental Health Data Archive.
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K.E.M., E.L.H. and T.A.B. conceptualized the study. K.E.M., E.L.H., T.A.B., J.B.N., J.J.W., A.C.R., N.S., R.D.R., M.G., M.M., S.S., D.C.K. and A.R.M. performed the experiments and analyzed data. K.E.M., T.A.B., N.S. and A.C.R. visualized the results. T.A.B., E.L.H. and E.R.M. contributed funding and resources. K.E.M., E.L.H., T.A.B., D.C.K. and R.S. contributed project administration support. Y.A., D.R.B., D.L.T., C.R.P., J.P., A.S., J. Lu, J. Leonard, A.P.O., A.P., C.H., M.E.H., E.L.H., M.B.B., O.R., E.Y., H.G.W.L., M.N.S., G.K.V.A., J.E.G. and D.C.K. provided patient data and samples, provided phenotypic data and interpreted clinical findings. K.E.M., D.C.K., E.L.H. and T.A.B. supervised the research. K.E.M., E.L.H. and T.A.B. wrote the original draft. All authors participated in review and editing of the manuscript.
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Extended data
Extended Data Fig. 1 Single-nuclei whole genome sequencing.
Whole genome sequencing of single-nuclei from Patient 1 brain tissue confirming the presence of chromosome 1q tetrasomy. Chromosome 1 copy number data is shown for representative nuclei with and without 1q tetrasomy (top) and the entire genome is shown (bottom) for the cell with the 1q gain.
Extended Data Fig. 2 Parental origin of chromosome 1q SNVs.
a, Variant allele fractions for SNVs found on chromosome 1q in Patient 1 brain, blood, buccal, and parental blood samples, demonstrating that these SNVs represent an extra chromosome 1q allele of maternal origin. b, OncoScan array results for Patient 1 trio demonstrating a chromosome 1q gain in proband brain tissue but no gain observed in blood samples from either parent, showing the parents are karyotypically normal. c, Variant allele fractions for a small number of representative chromosome 1q SNVs in available tissues from Patients 4, 5, and 6.
Extended Data Fig. 3 Mosaic chromosome 1q SNVs in patients with epilepsy or tumors.
a, Number of brain-restricted mosaic variants identified from exome sequencing of resected brain tissue versus blood samples from epilepsy Patients 1–6. b, Somatic variants identified from tumor-normal exome sequencing of various pediatric CNS tumors with chromosome 1q gains. No enrichment of variants on chromosome 1q is observed.
Extended Data Fig. 4 Inverted duplication of chromosome 1q in one patient.
a, A breakpoint-spanning read from PacBio HiFi long-read sequencing of Patient 2 brain DNA identifies the structure of the gain as an inverted duplication of chromosome 1q. b, Optical genome mapping coverage of the breakpoint.
Extended Data Fig. 5 Single-nuclei RNA-seq.
a, Single-nuclei RNA-seq quality control metrics: number of reads per nucleus, number of genes per nucleus, and percent mitochondrial reads. b, Feature plots showing expression of cell type markers.
Extended Data Fig. 6 Chromosome 1q gain in astrocytes.
a, InferCNV output for Patient 3 demonstrating the chromosome 1q gain enriched in astrocytes. b, Percent of cells with chromosome 1q gain depicted by patient and by cell type. c, Astrocytes with and without the chromosome 1q gain highly express astrocytic marker genes. d, InferCNV output comparing Patient 3 astrocytes from affected brain tissue to Patient 3 astrocytes from unaffected adjacent brain tissue. e, Fluorescence activated nuclei sorting based on PAX6-APC signal to enrich astrocytes followed by targeted sequencing of chromosome 1q marker SNVs in Patient 3. Astrocyte enriched cell population has increased representation of the chromosome 1q gain compared to bulk cells or PAX6-negative cells.
Extended Data Fig. 7 Gene expression differences between excitatory neurons with and without chromosome 1q gain.
a, Volcano plot showing differentially expressed genes in excitatory neurons with the chromosome 1q gain vs. those without. Black points represent genes located on chromosome 1q. b, Enriched GO terms for 1q gain excitatory neurons derived from an over-representation test performed with the enrichGO function of clusterprofiler R package with FDR p-value adjustment. c, Venn diagram showing overlap of differentially expressed genes with genes located on chromosome 1q.
Extended Data Fig. 8 Alternate models of isochromosome formation.
a, A potential model of mosaic isochromosome 1q formation in the early cleavage-stage embryo. b, An alternate model of mosaic isochromosome 1q formation originating in an oocyte.
Extended Data Fig. 9 Neuroimaging.
Brain MRIs from subjects with 1q duplications. a, b, Axial (a) and coronal (b) T2 images of Patient 1 at 13 months demonstrates hazy T2 prolongation involving the right frontal and parietal lobes (dashed circles). c, d, Axial (c) and coronal (d) T2 images of Patient 2 at 5 years of age demonstrate a dysplastic right frontal sulcus (dashed circles). e, f, Axial (e) and coronal (f) T2 images of Patient 3 at 9 months of age demonstrate polymicrogyria in the right frontal lobe and insula (dashed circle). g, h, Axial T1 (g) and axial T2 (h) images of Patient 6 at 14 months demonstrates hazy T1/T2 prolongation involving the inferior left frontal lobe (dashed circles). i, j, Axial T2 (i) and sagittal T1 (j) images of Patient 4 at 9 years of age demonstrate generalized decrease in size of the right hemisphere with a large frontoparietal area of dysplastic cortex (hazy T2 prolongation and increased gyral frequency indicated by dashed circles). k, l, Axial T2 (k) and coronal T2 (l) images of Patient 5 at 5 years of age demonstrate subtle T2 prolongation in the left supramarginal and superior temporal gyri (dashed circles).
Supplementary information
Supplementary Information
Supplementary Fig. 1.
Supplementary Data 1
1q mosaic variants identified in exome sequencing.
Supplementary Data 2
1q capture panel results for patient 3.
Supplementary Data 3
1q capture panel results for patient 1.
Supplementary Data 4
Deep targeted amplicon sequencing results for patients 1, 3, 4, 5 and 6.
Supplementary Data 5
Number of 1q gain versus no gain cells used for differential expression analysis per cell type and lists of differentially expressed genes identified per cell type.
Supplementary Data 6
Oligonucleotide sequences used for targeted sequencing assays.
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Miller, K.E., Rivaldi, A.C., Shinagawa, N. et al. Post-zygotic rescue of meiotic errors causes brain mosaicism and focal epilepsy. Nat Genet 55, 1920–1928 (2023). https://doi.org/10.1038/s41588-023-01547-z
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DOI: https://doi.org/10.1038/s41588-023-01547-z
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