Single-nucleus RNA-seq identifies Huntington disease astrocyte states

Osama Al-Dalahmah,Vilas Menon,James E Goldman,Kenneth Ofori,Istvan Adorjan,A Shaik,Alexander A Sosunov,Jean Paul Vonsattel,Yang Liu

doi:10.1186/s40478-020-0880-6

Osama Al-Dalahmah, Vilas Menon + Show 7 more

Open Access

https://doi.org/10.1186/s40478-020-0880-6

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Abstract

Huntington Disease (HD) is an inherited movement disorder caused by expanded CAG repeats in the Huntingtin gene. We have used single nucleus RNASeq (snRNASeq) to uncover cellular phenotypes that change in the disease, investigating single cell gene expression in cingulate cortex of patients with HD and comparing the gene expression to that of patients with no neurological disease. In this study, we focused on astrocytes, although we found significant gene expression differences in neurons, oligodendrocytes, and microglia as well. In particular, the gene expression profiles of astrocytes in HD showed multiple signatures, varying in phenotype from cells that had markedly upregulated metallothionein and heat shock genes, but had not completely lost the expression of genes associated with normal protoplasmic astrocytes, to astrocytes that had substantially upregulated glial fibrillary acidic protein (GFAP) and had lost expression of many normal protoplasmic astrocyte genes as well as metallothionein genes. When compared to astrocytes in control samples, astrocyte signatures in HD also showed downregulated expression of a number of genes, including several associated with protoplasmic astrocyte function and lipid synthesis. Thus, HD astrocytes appeared in variable transcriptional phenotypes, and could be divided into several different “states”, defined by patterns of gene expression. Ultimately, this study begins to fill the knowledge gap of single cell gene expression in HD and provide a more detailed understanding of the variation in changes in gene expression during astrocyte “reactions” to the disease.

Highlights

Huntington Disease (HD), a neurodegenerative disorder caused by CAG repeats in the Huntingtin gene, leads to the accumulation of the mutant protein and an associated neuronal degeneration and gliosis [34]
We examined the cingulate cortex, which is often affected in HD patients, because the cortical pathology is less severe than the neostriatal pathology, and because there is little known about cortical astrocyte pathology in HD
Genes involved in responses to metal ions, metal sequestration, and metallothionein binding were enriched in HD

Summary

Introduction

Huntington Disease (HD), a neurodegenerative disorder caused by CAG repeats in the Huntingtin gene, leads to the accumulation of the mutant protein and an associated neuronal degeneration and gliosis [34]. There are caudal-rostral and medial-lateral gradients of severity in the neostriatum [57], and relative sparing of the nucleus accumbens in advanced grade HD [44]. Astrocytes, in particular, are a key to maintaining the neuronal microenvironment, and display regional variation across the dorsal-ventral, rostral-caudal, and medial-lateral axes according to developmentally-determined domains [55]. Astrocytes in the affected regions of the HD brain show a “reactive” state, generally defined by histochemistry or by an increase in GFAP [48, 58], and by a decrease in the expression and protein levels of the major astrocytic glutamate transporter, EAAT2 [2, 9].

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