Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration

Vishnu Dileep; Carles A. Boix; Hansruedi Mathys; Asaf Marco; Gwyneth M. Welch; Hiruy S. Meharena; Anjanet Loon; Ritika Jeloka; Zhuyu Peng; David A. Bennett; Manolis Kellis; Li Huei Tsai

doi:10.1016/j.cell.2023.08.038

Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration

Vishnu Dileep^*, Carles A. Boix, Hansruedi Mathys, Asaf Marco, Gwyneth M. Welch, Hiruy S. Meharena, Anjanet Loon, Ritika Jeloka, Zhuyu Peng, David A. Bennett, Manolis Kellis^*, Li Huei Tsai^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

Persistent DNA double-strand breaks (DSBs) in neurons are an early pathological hallmark of neurodegenerative diseases including Alzheimer's disease (AD), with the potential to disrupt genome integrity. We used single-nucleus RNA-seq in human postmortem prefrontal cortex samples and found that excitatory neurons in AD were enriched for somatic mosaic gene fusions. Gene fusions were particularly enriched in excitatory neurons with DNA damage repair and senescence gene signatures. In addition, somatic genome structural variations and gene fusions were enriched in neurons burdened with DSBs in the CK-p25 mouse model of neurodegeneration. Neurons enriched for DSBs also had elevated levels of cohesin along with progressive multiscale disruption of the 3D genome organization aligned with transcriptional changes in synaptic, neuronal development, and histone genes. Overall, this study demonstrates the disruption of genome stability and the 3D genome organization by DSBs in neurons as pathological steps in the progression of neurodegenerative diseases.

Original language	American English
Pages (from-to)	4404-4421.e20
Journal	Cell
Volume	186
Issue number	20
DOIs	https://doi.org/10.1016/j.cell.2023.08.038
State	Published - 28 Sep 2023
Externally published	Yes

Bibliographical note

Funding Information:
This work was supported in part by NIH grants NS102730, NS051874, AG054012, Cure Alzheimer's Fund, JPB Foundation, and the Glenn Foundation for Aging Research to L.-H.T. NIH U01 NS110453 and NIH R01 AG058002 for M.K. and L.-H.T. V.D. was supported by NIH Pathway to Independence Award K99 AG073466 and Alzheimer's Association fellowship AARF-19-618751. C.A.B. was supported by NIH training grant GM087237. H.M. was supported by an Early Postdoc Mobility fellowship from the Swiss National Science Foundation (P2BSP3_151885). ROSMAP is supported by P30AG10161, P30AG72975, R01AG15819, R01AG17917. U01AG46152, U01AG61356 to D.A.B. ROSMAP resources can be requested at https://www.radc.rush.edu. We thank Dr. Ping-Chieh Pao, Dr. Jay Penny, Dr. Matheus Victor, Dr. William Ralvenius, the members of Tsai Lab, Dr. Maria Kousi, the members of Kellis Lab, and Dr. Vladimir Seplyarskiy for all the constructive discussions and feedback on the manuscript. We would also like to thank Ying Zhou and Erica McNamara of the Tsai Lab, Glenn Paradis and the team at Koch Institute Flow Cytometry Core, as well as Dr. Stuart Levine and the team at the MIT BioMicro Center. V.D. and L.-H.T. conceptualized and designed the project. V.D. performed and analyzed the Hi-C, BLISS, and mate-pair sequencing in CK-p25 and primary culture neurons. V.D. performed the tissue preparation and FACS sorting. C.A.B. performed the majority of the Smart-seq2, 10x RNA-seq, and ONT sequencing data analysis for gene fusions along with V.D. V.D. prepared Oxford nanopore libraries, and C.A.B. and V.D. analyzed the long read sequencing data. H.M. and Z.P. performed the human Smart-seq2 library preparation. V.D. and A.M. performed the P301S mice Hi-C library preparation. A.M. V.D. A.L. and R.J. performed immunostaining, imaging, and analysis. G.M.W. and H.S.M. helped with experimental design and setup. D.A.B. provided the human postmortem samples. V.D. C.A.B. M.K. and L.-H.T. wrote and revised the manuscript with input from all authors. L.-H.T. and M.K. provided the resources for the project. L.-H.T. is a member of the Scientific Advisory Board of Cognito Therapeutics, 4M Therapeutics, Cell Signaling Technology, and Souvien Therapeutics, which has no association to the work described in this manuscript. We support inclusive, diverse, and equitable conduct of research.

Funding Information:
This work was supported in part by NIH grants NS102730 , NS051874 , AG054012 , Cure Alzheimer's Fund , JPB Foundation , and the Glenn Foundation for Aging Research to L.-H.T. NIH U01 NS110453 and NIH R01 AG058002 for M.K. and L.-H.T. V.D. was supported by NIH Pathway to Independence Award K99 AG073466 and Alzheimer's Association fellowship AARF-19-618751 . C.A.B. was supported by NIH training grant GM087237 . H.M. was supported by an Early Postdoc Mobility fellowship from the Swiss National Science Foundation ( P2BSP3_151885 ). ROSMAP is supported by P30AG10161 , P30AG72975 , R01AG15819 , R01AG17917 . U01AG46152 , U01AG61356 to D.A.B. ROSMAP resources can be requested at https://www.radc.rush.edu . We thank Dr. Ping-Chieh Pao, Dr. Jay Penny, Dr. Matheus Victor, Dr. William Ralvenius, the members of Tsai Lab, Dr. Maria Kousi, the members of Kellis Lab, and Dr. Vladimir Seplyarskiy for all the constructive discussions and feedback on the manuscript. We would also like to thank Ying Zhou and Erica McNamara of the Tsai Lab, Glenn Paradis and the team at Koch Institute Flow Cytometry Core, as well as Dr. Stuart Levine and the team at the MIT BioMicro Center.

Publisher Copyright:
© 2023 The Authors

Keywords

3D genome organization
Alzheimer's disease
DNA double-strand breaks
epigenome
genome rearrangements
genomic mosaicism
neurodegeneration
senescence
structural variations
transcriptome

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1016/j.cell.2023.08.038

Cite this

@article{62f431df5fc3419c81460a57ff2fe747,

title = "Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration",

abstract = "Persistent DNA double-strand breaks (DSBs) in neurons are an early pathological hallmark of neurodegenerative diseases including Alzheimer's disease (AD), with the potential to disrupt genome integrity. We used single-nucleus RNA-seq in human postmortem prefrontal cortex samples and found that excitatory neurons in AD were enriched for somatic mosaic gene fusions. Gene fusions were particularly enriched in excitatory neurons with DNA damage repair and senescence gene signatures. In addition, somatic genome structural variations and gene fusions were enriched in neurons burdened with DSBs in the CK-p25 mouse model of neurodegeneration. Neurons enriched for DSBs also had elevated levels of cohesin along with progressive multiscale disruption of the 3D genome organization aligned with transcriptional changes in synaptic, neuronal development, and histone genes. Overall, this study demonstrates the disruption of genome stability and the 3D genome organization by DSBs in neurons as pathological steps in the progression of neurodegenerative diseases.",

keywords = "3D genome organization, Alzheimer's disease, DNA double-strand breaks, epigenome, genome rearrangements, genomic mosaicism, neurodegeneration, senescence, structural variations, transcriptome",

author = "Vishnu Dileep and Boix, {Carles A.} and Hansruedi Mathys and Asaf Marco and Welch, {Gwyneth M.} and Meharena, {Hiruy S.} and Anjanet Loon and Ritika Jeloka and Zhuyu Peng and Bennett, {David A.} and Manolis Kellis and Tsai, {Li Huei}",

note = "Funding Information: This work was supported in part by NIH grants NS102730, NS051874, AG054012, Cure Alzheimer's Fund, JPB Foundation, and the Glenn Foundation for Aging Research to L.-H.T. NIH U01 NS110453 and NIH R01 AG058002 for M.K. and L.-H.T. V.D. was supported by NIH Pathway to Independence Award K99 AG073466 and Alzheimer's Association fellowship AARF-19-618751. C.A.B. was supported by NIH training grant GM087237. H.M. was supported by an Early Postdoc Mobility fellowship from the Swiss National Science Foundation (P2BSP3_151885). ROSMAP is supported by P30AG10161, P30AG72975, R01AG15819, R01AG17917. U01AG46152, U01AG61356 to D.A.B. ROSMAP resources can be requested at https://www.radc.rush.edu. We thank Dr. Ping-Chieh Pao, Dr. Jay Penny, Dr. Matheus Victor, Dr. William Ralvenius, the members of Tsai Lab, Dr. Maria Kousi, the members of Kellis Lab, and Dr. Vladimir Seplyarskiy for all the constructive discussions and feedback on the manuscript. We would also like to thank Ying Zhou and Erica McNamara of the Tsai Lab, Glenn Paradis and the team at Koch Institute Flow Cytometry Core, as well as Dr. Stuart Levine and the team at the MIT BioMicro Center. V.D. and L.-H.T. conceptualized and designed the project. V.D. performed and analyzed the Hi-C, BLISS, and mate-pair sequencing in CK-p25 and primary culture neurons. V.D. performed the tissue preparation and FACS sorting. C.A.B. performed the majority of the Smart-seq2, 10x RNA-seq, and ONT sequencing data analysis for gene fusions along with V.D. V.D. prepared Oxford nanopore libraries, and C.A.B. and V.D. analyzed the long read sequencing data. H.M. and Z.P. performed the human Smart-seq2 library preparation. V.D. and A.M. performed the P301S mice Hi-C library preparation. A.M. V.D. A.L. and R.J. performed immunostaining, imaging, and analysis. G.M.W. and H.S.M. helped with experimental design and setup. D.A.B. provided the human postmortem samples. V.D. C.A.B. M.K. and L.-H.T. wrote and revised the manuscript with input from all authors. L.-H.T. and M.K. provided the resources for the project. L.-H.T. is a member of the Scientific Advisory Board of Cognito Therapeutics, 4M Therapeutics, Cell Signaling Technology, and Souvien Therapeutics, which has no association to the work described in this manuscript. We support inclusive, diverse, and equitable conduct of research. Funding Information: This work was supported in part by NIH grants NS102730 , NS051874 , AG054012 , Cure Alzheimer's Fund , JPB Foundation , and the Glenn Foundation for Aging Research to L.-H.T. NIH U01 NS110453 and NIH R01 AG058002 for M.K. and L.-H.T. V.D. was supported by NIH Pathway to Independence Award K99 AG073466 and Alzheimer's Association fellowship AARF-19-618751 . C.A.B. was supported by NIH training grant GM087237 . H.M. was supported by an Early Postdoc Mobility fellowship from the Swiss National Science Foundation ( P2BSP3_151885 ). ROSMAP is supported by P30AG10161 , P30AG72975 , R01AG15819 , R01AG17917 . U01AG46152 , U01AG61356 to D.A.B. ROSMAP resources can be requested at https://www.radc.rush.edu . We thank Dr. Ping-Chieh Pao, Dr. Jay Penny, Dr. Matheus Victor, Dr. William Ralvenius, the members of Tsai Lab, Dr. Maria Kousi, the members of Kellis Lab, and Dr. Vladimir Seplyarskiy for all the constructive discussions and feedback on the manuscript. We would also like to thank Ying Zhou and Erica McNamara of the Tsai Lab, Glenn Paradis and the team at Koch Institute Flow Cytometry Core, as well as Dr. Stuart Levine and the team at the MIT BioMicro Center. Publisher Copyright: {\textcopyright} 2023 The Authors",

year = "2023",

month = sep,

day = "28",

doi = "10.1016/j.cell.2023.08.038",

language = "American English",

volume = "186",

pages = "4404--4421.e20",

journal = "Cell",

issn = "0092-8674",

publisher = "Cell Press",

number = "20",

}

TY - JOUR

T1 - Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration

AU - Dileep, Vishnu

AU - Boix, Carles A.

AU - Mathys, Hansruedi

AU - Marco, Asaf

AU - Welch, Gwyneth M.

AU - Meharena, Hiruy S.

AU - Loon, Anjanet

AU - Jeloka, Ritika

AU - Peng, Zhuyu

AU - Bennett, David A.

AU - Kellis, Manolis

AU - Tsai, Li Huei

N1 - Funding Information: This work was supported in part by NIH grants NS102730, NS051874, AG054012, Cure Alzheimer's Fund, JPB Foundation, and the Glenn Foundation for Aging Research to L.-H.T. NIH U01 NS110453 and NIH R01 AG058002 for M.K. and L.-H.T. V.D. was supported by NIH Pathway to Independence Award K99 AG073466 and Alzheimer's Association fellowship AARF-19-618751. C.A.B. was supported by NIH training grant GM087237. H.M. was supported by an Early Postdoc Mobility fellowship from the Swiss National Science Foundation (P2BSP3_151885). ROSMAP is supported by P30AG10161, P30AG72975, R01AG15819, R01AG17917. U01AG46152, U01AG61356 to D.A.B. ROSMAP resources can be requested at https://www.radc.rush.edu. We thank Dr. Ping-Chieh Pao, Dr. Jay Penny, Dr. Matheus Victor, Dr. William Ralvenius, the members of Tsai Lab, Dr. Maria Kousi, the members of Kellis Lab, and Dr. Vladimir Seplyarskiy for all the constructive discussions and feedback on the manuscript. We would also like to thank Ying Zhou and Erica McNamara of the Tsai Lab, Glenn Paradis and the team at Koch Institute Flow Cytometry Core, as well as Dr. Stuart Levine and the team at the MIT BioMicro Center. V.D. and L.-H.T. conceptualized and designed the project. V.D. performed and analyzed the Hi-C, BLISS, and mate-pair sequencing in CK-p25 and primary culture neurons. V.D. performed the tissue preparation and FACS sorting. C.A.B. performed the majority of the Smart-seq2, 10x RNA-seq, and ONT sequencing data analysis for gene fusions along with V.D. V.D. prepared Oxford nanopore libraries, and C.A.B. and V.D. analyzed the long read sequencing data. H.M. and Z.P. performed the human Smart-seq2 library preparation. V.D. and A.M. performed the P301S mice Hi-C library preparation. A.M. V.D. A.L. and R.J. performed immunostaining, imaging, and analysis. G.M.W. and H.S.M. helped with experimental design and setup. D.A.B. provided the human postmortem samples. V.D. C.A.B. M.K. and L.-H.T. wrote and revised the manuscript with input from all authors. L.-H.T. and M.K. provided the resources for the project. L.-H.T. is a member of the Scientific Advisory Board of Cognito Therapeutics, 4M Therapeutics, Cell Signaling Technology, and Souvien Therapeutics, which has no association to the work described in this manuscript. We support inclusive, diverse, and equitable conduct of research. Funding Information: This work was supported in part by NIH grants NS102730 , NS051874 , AG054012 , Cure Alzheimer's Fund , JPB Foundation , and the Glenn Foundation for Aging Research to L.-H.T. NIH U01 NS110453 and NIH R01 AG058002 for M.K. and L.-H.T. V.D. was supported by NIH Pathway to Independence Award K99 AG073466 and Alzheimer's Association fellowship AARF-19-618751 . C.A.B. was supported by NIH training grant GM087237 . H.M. was supported by an Early Postdoc Mobility fellowship from the Swiss National Science Foundation ( P2BSP3_151885 ). ROSMAP is supported by P30AG10161 , P30AG72975 , R01AG15819 , R01AG17917 . U01AG46152 , U01AG61356 to D.A.B. ROSMAP resources can be requested at https://www.radc.rush.edu . We thank Dr. Ping-Chieh Pao, Dr. Jay Penny, Dr. Matheus Victor, Dr. William Ralvenius, the members of Tsai Lab, Dr. Maria Kousi, the members of Kellis Lab, and Dr. Vladimir Seplyarskiy for all the constructive discussions and feedback on the manuscript. We would also like to thank Ying Zhou and Erica McNamara of the Tsai Lab, Glenn Paradis and the team at Koch Institute Flow Cytometry Core, as well as Dr. Stuart Levine and the team at the MIT BioMicro Center. Publisher Copyright: © 2023 The Authors

PY - 2023/9/28

Y1 - 2023/9/28

N2 - Persistent DNA double-strand breaks (DSBs) in neurons are an early pathological hallmark of neurodegenerative diseases including Alzheimer's disease (AD), with the potential to disrupt genome integrity. We used single-nucleus RNA-seq in human postmortem prefrontal cortex samples and found that excitatory neurons in AD were enriched for somatic mosaic gene fusions. Gene fusions were particularly enriched in excitatory neurons with DNA damage repair and senescence gene signatures. In addition, somatic genome structural variations and gene fusions were enriched in neurons burdened with DSBs in the CK-p25 mouse model of neurodegeneration. Neurons enriched for DSBs also had elevated levels of cohesin along with progressive multiscale disruption of the 3D genome organization aligned with transcriptional changes in synaptic, neuronal development, and histone genes. Overall, this study demonstrates the disruption of genome stability and the 3D genome organization by DSBs in neurons as pathological steps in the progression of neurodegenerative diseases.

AB - Persistent DNA double-strand breaks (DSBs) in neurons are an early pathological hallmark of neurodegenerative diseases including Alzheimer's disease (AD), with the potential to disrupt genome integrity. We used single-nucleus RNA-seq in human postmortem prefrontal cortex samples and found that excitatory neurons in AD were enriched for somatic mosaic gene fusions. Gene fusions were particularly enriched in excitatory neurons with DNA damage repair and senescence gene signatures. In addition, somatic genome structural variations and gene fusions were enriched in neurons burdened with DSBs in the CK-p25 mouse model of neurodegeneration. Neurons enriched for DSBs also had elevated levels of cohesin along with progressive multiscale disruption of the 3D genome organization aligned with transcriptional changes in synaptic, neuronal development, and histone genes. Overall, this study demonstrates the disruption of genome stability and the 3D genome organization by DSBs in neurons as pathological steps in the progression of neurodegenerative diseases.

KW - 3D genome organization

KW - Alzheimer's disease

KW - DNA double-strand breaks

KW - epigenome

KW - genome rearrangements

KW - genomic mosaicism

KW - neurodegeneration

KW - senescence

KW - structural variations

KW - transcriptome

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U2 - 10.1016/j.cell.2023.08.038

DO - 10.1016/j.cell.2023.08.038

M3 - Article

C2 - 37774679

AN - SCOPUS:85172030416

SN - 0092-8674

VL - 186

SP - 4404-4421.e20

JO - Cell

JF - Cell

IS - 20

ER -

Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration

Abstract

Bibliographical note

Keywords

UN SDGs

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