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Updated: Apr 12, 2026
Purification of H3 and H4 Histone Proteins and the Quantification of Acetylated Histone Marks in Cells and Brain Tissue
Published on: November 30, 2018
Quantification of histone deacetylase isoforms in human frontal cortex, human retina, and mouse brain
Kyle W Anderson1, Junjun Chen2, Meiyao Wang2
1Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States of America; Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America; Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, United States of America.
Insights
Quantifying histone deacetylase (HDAC) isoforms in neurodegenerative diseases like Alzheimer's is crucial. This study developed a mass spectrometry assay revealing specific HDAC changes in human brain and retina, offering insights into disease pathology.
Area of Science:
- Neuroscience
- Biochemistry
- Mass Spectrometry
Background:
- Histone deacetylase (HDAC) inhibition shows therapeutic potential for neurodegenerative diseases.
- Current HDAC inhibitors lack specificity, targeting multiple isoforms with distinct functions.
- Understanding specific HDAC isoform expression is vital for targeted therapies.
Purpose of the Study:
- To develop and validate a quantitative assay for measuring HDAC isoforms in neural tissues.
- To determine the quantitative patterns of HDAC isoforms in human Alzheimer's disease (AD) and age-related macular degeneration (AMD).
- To compare HDAC profiles in human AD brain with a mouse model (5XFAD) of amyloid deposition.
Main Methods:
- Developed a multiple reaction monitoring (MRM) mass spectrometry assay.
- Utilized stable isotope-labeled QconCATs as internal standards for accurate quantification.
- Analyzed HDAC isoform concentrations in human frontal cortex, neural retina, and whole mouse brain.
Main Results:
- In human AD frontal cortex, HDAC1/2 decreased, while HDAC5/6 increased.
- HDAC isoform concentrations decreased in neural retina of AMD and AD patients.
- Significant differences observed between human AD brain and mouse models, with unique HDACs in mice.
Conclusions:
- The developed MRM assay is an efficient method for quantifying HDAC isoforms in various tissues and disease states.
- Specific alterations in HDAC isoform levels are associated with neurodegeneration in AD and AMD.
- HDAC profiling provides valuable insights into the molecular pathology of neurodegenerative diseases.
Abstract:
Histone deacetylase (HDAC) inhibition has promise as a therapy for Alzheimer's disease (AD) and other neurodegenerative diseases. Currently, therapeutic HDAC inhibitors target many HDAC isoforms, a particularly detrimental approach when HDAC isoforms are known to have different and specialized functions. We have developed a multiple reaction monitoring (MRM) mass spectrometry assay using stable isotope-labeled QconCATs as internal standards to quantify HDAC isoforms. We further determined a quantitative pattern of specific HDACs expressed in various human and mouse neural tissues. In human AD frontal cortex, HDAC1,2 decreased 32%, HDAC5 increased 47%, and HDAC6 increased 31% in comparison to age-matched controls. Human neural retina concentrations of HDAC1, 2, HDAC5, HDAC6, and HDAC7 decreased in age-related macular degeneration (AMD)-affected donors and exhibited a greater decrease in AD-affected donors in comparison to age-matched control neural retinas. Additionally, HDAC concentrations were measured in whole hemisphere of brain of 5XFAD mice, a model of β-amyloid deposition, to assess similarity to AD in human frontal cortex. HDAC profiles of human frontal cortex and mouse hemisphere had noticeable differences and relatively high concentrations of HDAC3 and HDAC4 in mice, which were undetectable in humans. Our method for quantification of HDAC isoforms is a practical and efficient technique to quantify isoforms in various tissues and diseases. Changes in HDAC concentrations reported herein contribute to the understanding of the pathology of neurodegeneration.
