*Result*: Combined somatic mutation and transcriptome analysis reveals region-specific differences in clonal architecture in human cortex.
Title:
Combined somatic mutation and transcriptome analysis reveals region-specific differences in clonal architecture in human cortex.
Authors:
Viswanadham VV; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Bioinformatics and Integrative Genomics Program, Harvard Medical School, Boston, MA, USA., Kim SN; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA., Caglayan E; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Doan RN; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA., Dou Y; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA., Bizzotto S; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Khoshkhoo S; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA., Huang AY; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Yeh R; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA., Chhouk BH; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA., Truong A; Research Computing, Harvard Medical School, Boston, MA, USA., Chappell KM; Research Computing, Harvard Medical School, Boston, MA, USA., Beaudin M; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA., Barton A; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Bioinformatics and Integrative Genomics Program, Harvard Medical School, Boston, MA, USA., Akula SK; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA., Zhao Y; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA, USA., Rento L; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA., Lodato M; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Szeto RA; Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA., Ganz J; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Li P; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Tsai JW; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA., Hill RS; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA., Park PJ; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. Electronic address: peter_park@hms.harvard.edu., Walsh CA; Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Department of Pediatrics, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA. Electronic address: christopher.walsh@childrens.harvard.edu.
Source:
Cell reports [Cell Rep] 2025 Nov 25; Vol. 44 (11), pp. 116458. Date of Electronic Publication: 2025 Nov 14.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Cell Press Country of Publication: United States NLM ID: 101573691 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2211-1247 (Electronic) NLM ISO Abbreviation: Cell Rep Subsets: MEDLINE
Imprint Name(s):
Original Publication: [Cambridge, MA] : Cell Press, c 2012-
MeSH Terms:
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J Can Acad Child Adolesc Psychiatry. 2011 Nov;20(4):265-76. (PMID: 22114608)
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Proc Natl Acad Sci U S A. 2021 Feb 23;118(8):. (PMID: 33593904)
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Science. 2015 Oct 2;350(6256):94-98. (PMID: 26430121)
Nature. 2021 Sep;597(7876):387-392. (PMID: 34433963)
J Comp Neurol. 1996 Mar 25;367(1):70-89. (PMID: 8867284)
Cereb Cortex. 2009 Feb;19(2):249-62. (PMID: 18477686)
Brain. 2004 Nov;127(Pt 11):2406-18. (PMID: 15319274)
Nat Commun. 2017 Jan 16;8:14049. (PMID: 28091601)
Nat Rev Neurosci. 2009 Oct;10(10):724-35. (PMID: 19763105)
Nature. 2024 May;629(8011):384-392. (PMID: 38600385)
J Anat. 2015 Oct;227(4):384-93. (PMID: 24839870)
Sci Rep. 2017 May 8;7(1):1567. (PMID: 28484262)
Nucleic Acids Res. 2017 Jun 2;45(10):e76. (PMID: 28132024)
J Neurosci. 2001 Jan 1;21(1):201-14. (PMID: 11150337)
Curr Opin Neurobiol. 2017 Feb;42:17-24. (PMID: 27889625)
Brain. 1980 Jun;103(2):221-44. (PMID: 6772266)
Cereb Cortex. 2017 Sep 1;27(9):4586-4606. (PMID: 28922855)
Nature. 2019 Sep;573(7772):61-68. (PMID: 31435019)
Cereb Cortex. 2011 Aug;21(8):1771-82. (PMID: 21139075)
Nature. 2001 Feb 8;409(6821):714-20. (PMID: 11217860)
Sci Rep. 2019 Dec 13;9(1):19123. (PMID: 31836783)
Cereb Cortex. 2009 Sep;19(9):2196-207. (PMID: 19234067)
Science. 2011 Oct 28;334(6055):480-6. (PMID: 22034427)
Nat Neurosci. 2013 Nov;16(11):1588-97. (PMID: 24097041)
Cereb Cortex. 2015 Mar;25(3):631-45. (PMID: 24047602)
Nature. 2009 Mar 26;458(7237):501-4. (PMID: 19204731)
Cell. 2014 Jun 19;157(7):1552-64. (PMID: 24949968)
Nat Neurosci. 1999 May;2(5):461-6. (PMID: 10321251)
Nat Rev Neurosci. 2006 Sep;7(9):687-96. (PMID: 16883309)
Proc Natl Acad Sci U S A. 2010 Sep 7;107(36):15927-32. (PMID: 20798050)
Genome Res. 2010 Sep;20(9):1297-303. (PMID: 20644199)
Nature. 2020 May;581(7809):434-443. (PMID: 32461654)
Cell Rep. 2014 Dec 24;9(6):2139-51. (PMID: 25497090)
BMC Evol Biol. 2018 Feb 2;18(1):11. (PMID: 29390973)
Nat Genet. 2016 Oct;48(10):1131-41. (PMID: 27595477)
Neuroimage. 2017 Jan;144(Pt B):270-274. (PMID: 27074495)
J Exp Med. 2007 Jan 22;204(1):17-23. (PMID: 17190840)
Development. 2013 Jul;140(13):2645-55. (PMID: 23757410)
Elife. 2020 Mar 05;9:. (PMID: 32134385)
Elife. 2022 Mar 15;11:. (PMID: 35289744)
Nat Neurosci. 2021 Feb;24(2):176-185. (PMID: 33432195)
Neuron. 2012 Jul 12;75(1):65-72. (PMID: 22794261)
Neuron. 2015 Jan 7;85(1):49-59. (PMID: 25569347)
Nat Methods. 2019 Dec;16(12):1289-1296. (PMID: 31740819)
Sci Rep. 2018 May 10;8(1):7476. (PMID: 29748573)
Proc Natl Acad Sci U S A. 2019 Dec 26;116(52):26173-26180. (PMID: 31871175)
Stem Cells. 2013 Jun;31(6):1193-201. (PMID: 23417928)
Proc Natl Acad Sci U S A. 2020 Jun 23;117(25):13886-13895. (PMID: 32522880)
Cereb Cortex. 2003 Oct;13(10):1072-83. (PMID: 12967924)
Nat Commun. 2019 Aug 14;10(1):3660. (PMID: 31413257)
Brain Res Dev Brain Res. 1991 Sep 19;62(1):137-41. (PMID: 1760867)
Nat Biotechnol. 2020 Mar;38(3):314-319. (PMID: 31907404)
Nature. 1989 Jan 19;337(6204):265-7. (PMID: 2536139)
Science. 1997 Oct 17;278(5337):474-6. (PMID: 9334308)
J Neurosci. 2010 Feb 3;30(5):1582-94. (PMID: 20130169)
Nature. 2002 Jun 6;417(6889):645-9. (PMID: 12050665)
Cell. 2014 Nov 6;159(4):775-88. (PMID: 25417155)
Front Cell Dev Biol. 2020 Oct 16;8:588814. (PMID: 33178700)
Development. 2001 Oct;128(19):3759-71. (PMID: 11585802)
Nat Methods. 2023 Sep;20(9):1323-1335. (PMID: 37550580)
J Neurosci. 2013 Jan 9;33(2):411-23. (PMID: 23303921)
Nature. 2012 May 02;486(7401):118-21. (PMID: 22678292)
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Neuron. 2018 Oct 24;100(2):294-313. (PMID: 30359598)
Nature. 2022 Jan;601(7893):397-403. (PMID: 34912114)
J Neurosci. 1999 Sep 15;19(18):7881-8. (PMID: 10479690)
Bioinformatics. 2011 Nov 1;27(21):2987-93. (PMID: 21903627)
Neuron. 2022 Dec 21;110(24):4043-4056.e5. (PMID: 36240767)
Nature. 2022 Jan;601(7893):404-409. (PMID: 34912118)
Neuron. 2015 Sep 2;87(5):989-98. (PMID: 26299473)
Genome Biol. 2021 Dec 2;22(1):329. (PMID: 34857027)
Neuron. 2015 Sep 2;87(5):999-1007. (PMID: 26299474)
Nat Biotechnol. 2024 Feb;42(2):293-304. (PMID: 37231261)
Nature. 1993 Dec 2;366(6454):464-6. (PMID: 8247154)
Proc Natl Acad Sci U S A. 1991 Mar 15;88(6):2083-7. (PMID: 2006147)
Science. 2022 Jul 8;377(6602):eabo0924. (PMID: 35737810)
Cell. 2012 Oct 26;151(3):483-96. (PMID: 23101622)
Epilepsia. 2005 Apr;46(4):556-60. (PMID: 15816950)
Nature. 2018 Sep;561(7724):473-478. (PMID: 30185910)
J Neurosci. 2012 Oct 31;32(44):15388-402. (PMID: 23115177)
Bioinformatics. 2020 Feb 1;36(3):742-750. (PMID: 31504211)
Cereb Cortex. 1999 Sep;9(6):636-45. (PMID: 10498282)
Epilepsia. 2015 Jan;56(1):66-76. (PMID: 25495786)
Nat Neurosci. 2013 Nov;16(11):1576-87. (PMID: 24097039)
Nature. 2025 Nov;647(8088):169-178. (PMID: 39779846)
Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5261-6. (PMID: 11959976)
J Comp Neurol. 2016 Feb 15;524(3):609-29. (PMID: 26304102)
Nature. 2021 May;593(7859):405-410. (PMID: 33911282)
Nature. 2013 Aug 22;500(7463):415-21. (PMID: 23945592)
Elife. 2019 Nov 18;8:. (PMID: 31736464)
Bioinformatics. 2017 Sep 15;33(18):2938-2940. (PMID: 28645171)
BMC Bioinformatics. 2015 Jan 16;16:10. (PMID: 25592313)
J Neurosci. 2015 Oct 21;35(42):14307-15. (PMID: 26490868)
Science. 2021 Mar 19;371(6535):1245-1248. (PMID: 33737484)
J Can Acad Child Adolesc Psychiatry. 2011 Nov;20(4):265-76. (PMID: 22114608)
Development. 1997 Jun;124(12):2441-50. (PMID: 9199370)
BMC Med Genomics. 2021 Feb 12;14(1):47. (PMID: 33579278)
Development. 2001 Feb;128(3):353-63. (PMID: 11152634)
Proc Natl Acad Sci U S A. 2021 Feb 23;118(8):. (PMID: 33593904)
Bioinformatics. 2010 Mar 15;26(6):841-2. (PMID: 20110278)
Nature. 2016 Aug 11;536(7615):171-178. (PMID: 27437579)
PLoS One. 2013 May 28;8(5):e63848. (PMID: 23724007)
Front Cell Dev Biol. 2021 May 13;9:676911. (PMID: 34055808)
Front Neuroanat. 2014 Sep 25;8:103. (PMID: 25309344)
Nature. 2022 Apr;604(7907):689-696. (PMID: 35444276)
Neuron. 2019 Sep 25;103(6):980-1004. (PMID: 31557462)
Cereb Cortex. 2002 Jan;12(1):37-53. (PMID: 11734531)
Nat Neurosci. 2001 Sep;4(9):931-6. (PMID: 11528425)
Science. 2021 Mar 19;371(6535):1249-1253. (PMID: 33737485)
Cell. 2022 Jan 20;185(2):311-327.e24. (PMID: 35063073)
Neuron. 2005 Aug 4;47(3):353-64. (PMID: 16055060)
Science. 2015 Oct 2;350(6256):94-98. (PMID: 26430121)
Nature. 2021 Sep;597(7876):387-392. (PMID: 34433963)
J Comp Neurol. 1996 Mar 25;367(1):70-89. (PMID: 8867284)
Cereb Cortex. 2009 Feb;19(2):249-62. (PMID: 18477686)
Brain. 2004 Nov;127(Pt 11):2406-18. (PMID: 15319274)
Grant Information:
F31 CA264958 United States CA NCI NIH HHS; U01 MH106883 United States MH NIMH NIH HHS; T15 LM007092 United States LM NLM NIH HHS; UH3 NS132144 United States NS NINDS NIH HHS; K08 NS128272 United States NS NINDS NIH HHS; United States HHMI Howard Hughes Medical Institute; R01 NS032457 United States NS NINDS NIH HHS; L30 NS118655 United States NS NINDS NIH HHS
Contributed Indexing:
Keywords: CP: genomics; CP: neuroscience; cortical development; glutamatergic neurons; interneurons; lineage tracing; single-cell transcriptomics; somatic mutations; spatial genomics; visual cortex
Entry Date(s):
Date Created: 20251115 Date Completed: 20251129 Latest Revision: 20260307
Update Code:
20260307
PubMed Central ID:
PMC12766648
DOI:
10.1016/j.celrep.2025.116458
PMID:
41240340
Database:
MEDLINE
*Further Information*
*The human cerebral cortex is specialized into regions, but little is known about how human cellular lineages shape cortical regional variation and neuronal cell-type distribution during development. Here, we map single-cell lineages of human cortical regions and neuronal subtypes using >1,000 somatic single-nucleotide variants (sSNVs) identified from deep bulk whole-genome sequencing and analyzed over 25 regions and >72,000 single cells. In the fronto-parietal cortex, sSNVs are rarely restricted, marking neuron-generating clones that disperse into neighboring regions. In contrast, the primary visual cortex harbors 30%-70% more sSNVs than the neighboring secondary visual cortex. Clones at this border exhibit more restricted dispersion, suggesting late developmental lineage segregation. Single-nucleus sSNV and whole-transcriptome analysis reveal glutamatergic neuron clones with modest regional restrictions that share low-mosaic sSNVs with some GABAergic neurons, suggesting a recent dorsal cortical progenitor. Our analysis reveals human-specific cortical lineage patterns, regional differences in clonal patterns, and late divergence of some glutamatergic/GABAergic lineages.
(Copyright © 2025 The Author(s). Published by Elsevier Inc. All rights reserved.)*
*Declaration of interests C.A.W. and P.J.P. are on the scientific advisory board (SAB) of Bioskryb Genomics (cash and equity), and C.A.W. is on the SAB of Mosaica Therapeutics (cash and equity) and is an advisor to Maze Therapeutics (equity).*