Cited by 408Genetic Neurodegenerative DiseasesGenetics and Neurodevelopmental DisordersNeurological diseases and metabolism

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Integrated genomics and proteomics define huntingtin CAG length-dependent networks in mice

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Langfelder, Peter, Cantle, Jeffrey P, Chatzopoulou, Doxa, Wang, Nan, Gao, Fuying, Al-Ramahi, Ismael, Lu, Xiao-Hong, Ramos, Eliana Marisa, El-Zein, Karla, Zhao, Yining, Deverasetty, Sandeep, Tebbe, Andreas, Schaab, Christoph, Lavery, Daniel J, Howland, David, Kwak, Seung, Botas, Juan, Aaronson, Jeffrey S, Rosinski, Jim, Coppola, Giovanni, Horvath, Steve, Yang, X William·2016·Nature Neuroscience

DOI 10.1038/nn.4256PMC PMC5984042

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Abstract

To gain insight into how mutant huntingtin (mHtt) CAG repeat length modifies Huntington's disease (HD) pathogenesis, we profiled mRNA in over 600 brain and peripheral tissue samples from HD knock-in mice with increasing CAG repeat lengths. We found repeat length-dependent transcriptional signatures to be prominent in the striatum, less so in cortex, and minimal in the liver. Coexpression network analyses revealed 13 striatal and 5 cortical modules that correlated highly with CAG length and age, and that were preserved in HD models and sometimes in patients. Top striatal modules implicated mHtt CAG length and age in graded impairment in the expression of identity genes for striatal medium spiny neurons and in dysregulation of cyclic AMP signaling, cell death and protocadherin genes. We used proteomics to confirm 790 genes and 5 striatal modules with CAG length-dependent dysregulation at the protein level, and validated 22 striatal module genes as modifiers of mHtt toxicities in vivo.

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Additional file 7 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003539
Additional file 3 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003524
Additional file 2 of Brain microvascular endothelial cell dysfunction in an isogenic juvenile iPSC model of Huntington’s disease
Linville, R. M., Nerenberg, R. F., Grifno, G. N., Arevalo, D., Guo, Z., & Searson, P. C. (2022) · Figshare · doi:10.6084/m9.figshare.20208314
Additional file 10 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003491
Additional file 8 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003542
Additional file 14 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003503
Additional file 13 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003500
Additional file 15 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003506
Additional file 12 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003497
Additional file 4 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003527
Additional file 5 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003530
Additional file 6 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003533
Additional file 2 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003521
Additional file 1 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003515
Additional file 16 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003509
Additional file 18 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003512
Additional file 1 of Cerebellar granule neurons induce Cyclin D1 before the onset of motor symptoms in Huntington’s disease mice
Bauer, S., Chen, C.-Y., Jonson, M., Kaczmarczyk, L., Magadi, S. S., & Jackson, W. S. (2024) · Figshare · doi:10.6084/m9.figshare.26562985
Additional file 11 of CK2 alpha prime and alpha-synuclein pathogenic functional interaction mediates synaptic dysregulation in Huntington’s disease
Yu, D., Zarate, N., White, A., Coates, D., Tsai, W., Nanclares, C., Cuccu, F., Yue, J. S., Brown, T. G., Mansky, R. H., et al. (2022) · Figshare · doi:10.6084/m9.figshare.20003494
Temporal single-cell atlas of full-length Huntington’s disease mouse model defines stage-specific signatures of corticostriatal dysfunctionPreprint
Robbins, A. B., Ranum, P. T., Huerta-Ocampo, I., Kuckyr, M., & Davidson, B. L. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.07.698249
Mouse models to interrogate the developmental pathogenesis of Huntington's disease
Altun, Y., Yan, S., Zheng, K., Molero, A. E., & Mehler, M. F. (2026) · Journal of Huntington s Disease · doi:10.1177/18796397251412135 · Cited by 1
High-throughput quantification of huntingtin mRNA expression and aggregation in mouse brain using automated RNAscope imagingPreprint
van Velde, P., Tran, B., Allen, S., Luu, E., Furgal, R. C., Summers, A., Belgrad, J., Knox, E. G., Khvorova, A., & Grünwald, D. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.09.704866
Contribution of neuroepigenetics to HD – developmental and aging-related signatures
Scuto, J., Penaud, N., & Mérienne, K. (2026) · Journal of Huntington s Disease · doi:10.1177/18796397261426625
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Langfelder, P., Wang, N., Ramanathan, L., Oh, Y. M., Lee, S., Gao, F., Gu, X., Stricos, M., Plascencia, M., Vaca, R., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.02.709091
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Développement de l’imagerie métabolique par IRM-CEST : application à la maladie de Huntington
Pépin, J. (2018) · theses.fr (ABES) · doi:10.70675/36f26e42z6133z47dbz84a3z07fae7850aa0
Role of the cholesterol hydroxylase enzyme CYP46A1 in cholesterol metabolism and neuroprotection in Huntington's disease
Kacher, R. (2019) · theses.fr (ABES) · doi:10.70675/2e6ac10bz0700z4936z81f8z18565a62aaf5
Les astrocytes réactifs, des partenaires anti-agrégants dans la maladie de Huntington : identification des mécanismes impliqués dans le dialogue neurone-astrocyte
Abjean, L. (2019) · theses.fr (ABES) · doi:10.70675/f664e003zf93fz467eza6a3z3d953eaffe4e
Etude du rôle de la protéine kinase DCLK3 dans les mécanismes de neurodégénérescence dans la maladie de Huntington
de Longprez, L. (2018) · theses.fr (ABES) · doi:10.70675/9c720f01z8077z49d5z9df8z8e7cc0c69a1a
Rôle des altérations transcriptionnelles et épigénétiques dans les déficits comportementaux de la maladie de Huntington
Lotz, C. (2019) · theses.fr (ABES) · doi:10.70675/35213e27zda27z484az886azd1ed4013e75a
The role of the serum response factor in the pathogenesis of Huntington's disease
Awada, A. (2021) · theses.fr (ABES) · doi:10.70675/fabef4b5z9d78z440bz99f2z9be7d0814a03
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Belgrad, J., Summers, A., Hildebrand, S. R., Sapp, E., Luu, E., Yamada, N., O’Reilly, D., Vogt, T., Howland, D., Yang, X. W., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.08.723329
Self-citation

Authors: Langfelder, P., Cantle, J. P., Chatzopoulou, D., Wang, N., Gao, F., Al-Ramahi, I., Lu, X.-H., Ramos, E. M., El-Zein, K., Zhao, Y., Deverasetty, S., Tebbe, A., Schaab, C., Lavery, D. J., Howland, D., Kwak, S., Botas, J., Aaronson, J. S., Rosinski, J., Coppola, G., Horvath, S., & Yang, X. W.
Affiliations: University of California, Los Angeles (US)
Evotec (Germany) (DE)
CHDI Foundation (US)
Baylor College of Medicine (US)
Corresponding author: Horvath, Steve
Yang, X William
ORCID: Langfelder, Peter
Cantle, Jeffrey P
Wang, Nan
Gao, Fuying
Lu, Xiao-Hong
Ramos, Eliana Marisa
Zhao, Yining
Schaab, Christoph
Lavery, Daniel J
Howland, David
Kwak, Seung
Botas, Juan
Coppola, Giovanni
Horvath, Steve
Yang, X William
Venue: Nature Neuroscience
Publisher: Springer Science and Business Media LLC
Published: 2016-02-22
Volume: 19
Issue: 4
Pages: 623-633
ISSN: 1097-6256 (ISSN-L)
1546-1726
DOI: 10.1038/nn.4256
PMC: PMC5984042
OpenAlex: W2274495055
Cited by: 385
References: 74
Citations by year: 2026: 29 · 2025: 27 · 2024: 30 · 2023: 30 · 2022: 60 · 2021: 40 · 2020: 40 · 2019: 36 · 2018: 36 · 2017: 41 · 2016: 16
FWCI: 19.76
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature Neuroscience (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
eScholarship (California Digital Library) (submittedVersion)
Funders: Hereditary Disease Foundation
CHDI Foundation
National Institutes of Health
National Institute of Neurological Disorders and Stroke (R01NS084298, R01NS049501, R01NS074312, P30NS062691)
Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles
Topics: Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Genetic Neurodegenerative Diseases
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
Life Sciences › Neuroscience › Neurology › Neurological diseases and metabolism
Keywords: Huntington's disease, mutant huntingtin, CAG repeat length, repeat expansion, transcriptome, proteome, co-expression network, striatum, medium spiny neurons, cAMP signaling, protocadherins, cell death, age-related gene expression, disease-modifying genes, knock-in mice
MeSH terms: Huntingtin Protein, Animals, Cerebral Cortex, Corpus Striatum, Female, Male, Mice, Inbred C57BL, Nerve Tissue Proteins, Nuclear Proteins, Genomics, Proteomics, Mice, Gene Regulatory Networks, Gene Knock-In Techniques

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Integrated genomics and proteomics define huntingtin CAG length-dependent networks in mice

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