Histone deacetylase knockouts modify transcription, CAG instability and nuclear pathology in Huntington disease mice

  1. Marina Kovalenko
  2. Serkan Erdin
  3. Marissa A Andrew
  4. Jason St Claire
  5. Melissa Shaughnessey
  6. Leroy Hubert
  7. João Luís Neto
  8. Alexei Stortchevoi
  9. Daniel M Fass
  10. Ricardo Mouro Pinto
  11. Stephen J Haggarty
  12. John H Wilson
  13. Michael E Talkowski
  14. Vanessa C Wheeler  Is a corresponding author
  1. Massachusetts General Hospital, United States
  2. Massachusetts General Hospital/Broad Institute, United States
  3. Baylor College of Medicine, United States
  4. Massachusetts General Hospital, Harvard Medical School, United States

Abstract

Somatic expansion of the Huntington's disease (HD) CAG repeat drives the rate of a pathogenic process ultimately resulting in neuronal cell death. Although mechanisms of toxicity are poorly delineated, transcriptional dysregulation is a likely contributor. To identify modifiers that act at the level of CAG expansion and/or downstream pathogenic processes, we tested the impact of genetic knockout, in HttQ111 mice, of Hdac2 or Hdac3 in medium-spiny striatal neurons that exhibit extensive CAG expansion and exquisite disease vulnerability. Both knockouts moderately attenuated CAG expansion, with Hdac2 knockout decreasing nuclear huntingtin pathology. Hdac2 knockout resulted in a substantial transcriptional response that included modification of transcriptional dysregulation elicited by the HttQ111 allele, likely via mechanisms unrelated to instability suppression. Our results identify novel modifiers of different aspects of HD pathogenesis in MSNs and highlight a complex relationship between the expanded Htt allele and Hdac2 with implications for targeting transcriptional dysregulation in HD.

Data availability

RNA-Seq data is deposited in GEO, under the accession number GSE148440

The following data sets were generated

Article and author information

Author details

  1. Marina Kovalenko

    Center for Genomic Medicine, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  2. Serkan Erdin

    Center for Genomic Medicine/Program in Medical and Population Genetics, Massachusetts General Hospital/Broad Institute, Boston, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6587-2625
  3. Marissa A Andrew

    Center for Genomic Medicine, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  4. Jason St Claire

    Center for Genomic Medicine, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  5. Melissa Shaughnessey

    Center for Genomic Medicine; Department of Neurology, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  6. Leroy Hubert

    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States
    Competing interests
    No competing interests declared.
  7. João Luís Neto

    Center for Genomic Medicine; Department of Neurology, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0863-158X
  8. Alexei Stortchevoi

    Center for Genomic Medicine, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  9. Daniel M Fass

    Center for Genomic Medicine, Massachusetts General Hospital, Boston, United States
    Competing interests
    Daniel M Fass, D.M.F. is a member of the scientific advisory board of Psy Therapeutics..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0018-8093
  10. Ricardo Mouro Pinto

    Center for Genomic Medicine; Department of Neurology, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  11. Stephen J Haggarty

    Chemical Neurobiology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, United States
    Competing interests
    Stephen J Haggarty, S.J.H. is a member of the scientific advisory board of Psy Therapeutics, Frequency Therapeutics and Souvien Therapeutics, and former member of the scientific advisory board of Rodin Therapeutics that is focused on HDAC2 inhibitors, none of whom were involved in the present study. S.J.H. has also received speaking or consulting fees from Amgen, AstraZeneca, Biogen, Merck, Regenacy Pharmaceuticals, as well as sponsored research or gift funding from AstraZeneca, JW Pharmaceuticals, and Vesigen unrelated to the content of this manuscript. His financial interests were reviewed and are managed by Massachusetts General Hospital and Partners HealthCare in accordance with their conflict of interest policies..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7872-168X
  12. John H Wilson

    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, United States
    Competing interests
    No competing interests declared.
  13. Michael E Talkowski

    Center for Genomic Medicine/Program in Medical and Population Genetics, Massachusetts General Hospital/Broad Institute, Boston, United States
    Competing interests
    No competing interests declared.
  14. Vanessa C Wheeler

    Center for Genomic Medicine; Department of Neurology, Massachusetts General Hospital, Boston, United States
    For correspondence
    wheeler@helix.mgh.harvard.edu
    Competing interests
    Vanessa C Wheeler, V.C.W is a scientific advisory board member of Triplet Therapeutics, a company developing new therapeutic approaches to address triplet repeat disorders such Huntington's disease and Myotonic Dystrophy and of LoQus23 Therapeutics. Her financial interests in Triplet Therapeutics, were reviewed and are managed by Massachusetts General Hospital and Partners HealthCare in accordance with their conflict of interest policies..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2619-589X

Funding

Huntington Society of Canada (New Pathways Research Grant)

  • Vanessa C Wheeler

National Institutes of Health (NS049206)

  • Vanessa C Wheeler

Huntington's Disease Society of America (Berman Topper Career Development Award)

  • Ricardo Mouro Pinto

National Institutes of Health (GM38219)

  • John H Wilson

National Institutes of Health (EY11731)

  • John H Wilson

National Institutes of Health (1F3HG004918)

  • Leroy Hubert

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Harry T Orr, University of Minnesota, United States

Ethics

Animal experimentation: This study was carried out in accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health under an approved protocol (2009N000216) of the Massachusetts General Hospital Subcommittee on Research Animal Care.

Version history

  1. Received: April 15, 2020
  2. Accepted: September 28, 2020
  3. Accepted Manuscript published: September 29, 2020 (version 1)
  4. Version of Record published: October 22, 2020 (version 2)

Copyright

© 2020, Kovalenko et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,085
    views
  • 295
    downloads
  • 6
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Marina Kovalenko
  2. Serkan Erdin
  3. Marissa A Andrew
  4. Jason St Claire
  5. Melissa Shaughnessey
  6. Leroy Hubert
  7. João Luís Neto
  8. Alexei Stortchevoi
  9. Daniel M Fass
  10. Ricardo Mouro Pinto
  11. Stephen J Haggarty
  12. John H Wilson
  13. Michael E Talkowski
  14. Vanessa C Wheeler
(2020)
Histone deacetylase knockouts modify transcription, CAG instability and nuclear pathology in Huntington disease mice
eLife 9:e55911.
https://doi.org/10.7554/eLife.55911

Share this article

https://doi.org/10.7554/eLife.55911

Further reading

    1. Genetics and Genomics
    David V Ho, Duncan Tormey ... Peter Baumann
    Research Article

    Facultative parthenogenesis (FP) has historically been regarded as rare in vertebrates, but in recent years incidences have been reported in a growing list of fish, reptile, and bird species. Despite the increasing interest in the phenomenon, the underlying mechanism and evolutionary implications have remained unclear. A common finding across many incidences of FP is either a high degree of homozygosity at microsatellite loci or low levels of heterozygosity detected in next-generation sequencing data. This has led to the proposal that second polar body fusion following the meiotic divisions restores diploidy and thereby mimics fertilization. Here, we show that FP occurring in the gonochoristic Aspidoscelis species A. marmoratus and A. arizonae results in genome-wide homozygosity, an observation inconsistent with polar body fusion as the underlying mechanism of restoration. Instead, a high-quality reference genome for A. marmoratus and analysis of whole-genome sequencing from multiple FP and control animals reveals that a post-meiotic mechanism gives rise to homozygous animals from haploid, unfertilized oocytes. Contrary to the widely held belief that females need to be isolated from males to undergo FP, females housed with conspecific and heterospecific males produced unfertilized eggs that underwent spontaneous development. In addition, offspring arising from both fertilized eggs and parthenogenetic development were observed to arise from a single clutch. Strikingly, our data support a mechanism for facultative parthenogenesis that removes all heterozygosity in a single generation. Complete homozygosity exposes the genetic load and explains the high rate of congenital malformations and embryonic mortality associated with FP in many species. Conversely, for animals that develop normally, FP could potentially exert strong purifying selection as all lethal recessive alleles are purged in a single generation.

    1. Genetics and Genomics
    Weiting Zhang, Karl Petri ... Jing-Ruey Joanna Yeh
    Short Report

    CRISPR prime editing (PE) requires a Cas9 nickase-reverse transcriptase fusion protein (known as PE2) and a prime editing guide RNA (pegRNA), an extended version of a standard guide RNA (gRNA) that both specifies the intended target genomic sequence and encodes the desired genetic edit. Here, we show that sequence complementarity between the 5’ and the 3’ regions of a pegRNA can negatively impact its ability to complex with Cas9, thereby potentially reducing PE efficiency. We demonstrate this limitation can be overcome by a simple pegRNA refolding procedure, which improved ribonucleoprotein-mediated PE efficiencies in zebrafish embryos by up to nearly 25-fold. Further gains in PE efficiencies of as much as sixfold could also be achieved by introducing point mutations designed to disrupt internal interactions within the pegRNA. Our work defines simple strategies that can be implemented to improve the efficiency of PE.