Lodato Lab

2023

Single-cell transcriptomic and genomic changes in the aging human brain

A. M. Jeffries*, T. Yu*, J. S. Ziegenfuss, A. Tolles, Y. Kim, Z. Weng#, and M. A. Lodato#

bioRxiv 2023.11.07.566050; doi: https://doi.org/10.1101/2023.11.07.566050

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Somatic mutations, genome mosaicism and aging

M. A. Lodato# and J. Vijg#

Frontiers in Aging 3, 1115408 10.3389/fragi.2022.1115408

 

2022

Somatic genomic changes in single Alzheimer's disease neurons

M. B. Miller*, A. Y. Huang*, J. Kim, Z. Zhou, S. L. Kirkham, E. A. Maury, J. S. Ziegenfuss, H. C. Reed, J. E. Neil, L. Rento, S. C. Ryu, C. C. Ma, L. J. Luquette, H. M. Ames, D. H. Oakley, M. P. Frosch, B. T. Hyman, M. A. Lodato#, E. A. Lee#and C. A. Walsh#

Nature 604, 714-722 10.1038/s41586-022-04640-1. Covered in The Boston Globe, AlzForum, U.S. News and World Report, and others.

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Persistent DNA damage associated with ATM kinase deficiency promotes microglial dysfunction

J. Bourseguin, W. Cheng, E. Talbot, L. Hardy, J. Lai, A. M. Jeffries, M. A. Lodato, E. A. Lee and S. V. Khoronenkova

Nucleic Acids Research 50, 2700-2718 10.1093/nar/gkac104

 

Somatic mutations in single human cardiomyocytes reveal age-associated DNA damage and widespread oxidative genotoxicity

S. Choudhury, A. Y. Huang, J. Kim, Z. Zhou, K. Morillo, E. A. Maury, J. W. Tsai, M. B. Miller, M. A. Lodato, S. Araten, N. Hilal, E. A. Lee#, M. H. Chen# and C. A. Walsh#

Nature Aging 2, 714-725 10.1038/s43587-022-00261-5

 

Prevalence and mechanisms of somatic deletions in single human neurons during normal aging and in DNA repair disorders

J. Kim, A. Y. Huang, S. L. Johnson, J. Lai, L. Isacco, A. M. Jeffries, M. B. Miller, M. A. Lodato, C. A. Walsh# and E. A. Lee#

Nature Communications 13, 5918 10.1038/s41467-022-33642-w

 

The two faces of DNA oxidation in genomic and functional mosaicism during aging in human neurons

J. S. Ziegenfuss and M. A. Lodato

Frontiers in Aging 3, 991460 10.3389/fragi.2022.991460

 

Single-cell genome sequencing of human neurons identifies somatic point mutation and indel enrichment in regulatory elements

L. J. Luquette*, M. B. Miller*, Z. Zhou, C. L. Bohrson, Y. Zhao, H. Jin, D. Gulhan, J. Ganz, S. Bizzotto, S. Kirkham, T. Hochepied, C. Libert, A. Galor, J. Kim, M. A. Lodato, J. I. Garaycoechea, C. Gawad, J. West, C. A. Walsh# and P. J. Park#

Nature Genetics 54, 1564-1571 10.1038/s41588-022-01180-2

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2021

Single-nucleus transcriptomic analyses reveal microglial activation underlying cerebellar degeneration in Ataxia Telangiectasia

J. Lai, J. Kim, A. M. Jeffries, A. Tolles, T. W. Chittenden, P. G. Buckley, T. W. Yu, M. A. Lodato# and E. A. Lee#

bioRxiv, 2021.09.09.459619 10.1101/2021.09.09.459619

 

2020

APP gene copy number changes reflect exogenous contamination

J. Kim, B. Zhao, A. Y. Huang, M. B. Miller, M. A. Lodato, C. A. Walsh# and E. A. Lee#

Nature 584, E20-E28 10.1038/s41586-020-2522-3

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2019

Linked-read analysis identifies mutations in single-cell DNA-sequencing data

C. L. Bohrson, A. R. Barton, M. A. Lodato, R. E. Rodin, L. J. Luquette, V. V. Viswanadham, D. C. Gulhan, I. Cortes-Ciriano, M. A. Sherman, M. Kwon, M. E. Coulter, A. Galor, C. A. Walsh and P. J. Park

Nature Genetics 51, 749-754 10.1038/s41588-019-0366-2

 

Genome aging: somatic mutation in the brain links age-related decline with disease and nominates pathogenic mechanisms

M. A. Lodato and C. A. Walsh

Human Molecular Genetics 28, R197-R206 10.1093/hmg/ddz191

 

 2018 

Aging and neurodegeneration are associated with increased mutations in single human neurons

M. A. Lodato*, R. E. Rodin*, C. L. Bohrson*, M. E. Coulter*, A. R. Barton*, M. Kwon*, M. A. Sherman, C. M. Vitzthum, L. J. Luquette, C. Yandava, P. Yang, T. W. Chittenden, N. E. Hatem, S. C. Ryu, M. B. Woodworth, P. J. Park# and C. A. Walsh#

Science 359, 555-559 10.1126/science.aao4426. Covered in Yahoo! News, GenomeWeb, and others.

 

2017

Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network

M. J. McConnell, J. V. Moran, A. Abyzov, S. Akbarian, T. Bae, I. Cortes-Ciriano, J. A. Erwin, L. Fasching, D. A. Flasch, D. Freed, J. Ganz, A. E. Jaffe, K. Y. Kwan, M. Kwon, M. A. Lodato, R. E. Mills, A. C. M. Paquola, R. E. Rodin, C. Rosenbluh, N. Sestan, M. A. Sherman, J. H. Shin, S. Song, R. E. Straub, J. Thorpe, D. R. Weinberger, A. E. Urban, B. Zhou, F. H. Gage, T. Lehner, G. Senthil, C. A. Walsh, A. Chess, E. Courchesne, J. G. Gleeson, J. M. Kidd, P. J. Park, J. Pevsner, F. M. Vaccarino and N. Brain Somatic Mosaicism Network

Science 35610.1126/science.aal1641

 

PaSD-qc: quality control for single cell whole-genome sequencing data using power spectral density estimation

M. A. Sherman, A. R. Barton, M. A. Lodato, C. Vitzthum, M. E. Coulter, C. A. Walsh and P. J. Park

Nucleic Acids Research10.1093/nar/gkx1195

 

2015

Somatic mutation in single human neurons tracks developmental and transcriptional history

M. A. Lodato*, M. B. Woodworth*, S. Lee*, G. D. Evrony, B. K. Mehta, A. Karger, S. Lee, T. W. Chittenden, A. M. D'Gama, X. Cai, L. J. Luquette, E. Lee, P. J. Park# and C. A. Walsh#

Science 350, 94-8.

Covered in the Wall Street Journal, The Atlantic, Science, Scientific American, and others.

 

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