The dynamics of early-state transcriptional changes and aggregate formation in a Huntington’s disease cell model

Abstract

BackgroundHuntington’s disease (HD) is a fatal neurodegenerative disorder caused by a CAG expansion in the Huntingtin (HTT) gene. Proteolytic cleavage of mutant huntingtin (Htt) protein with an expanded polyglutamine (polyQ) stretch results in production of Htt fragments that aggregate and induce impaired ubiquitin proteasome, mitochondrial functioning and transcriptional dysregulation. To understand the time-resolved relationship between aggregate formation and transcriptional changes at early disease stages, we performed temporal transcriptome profiling and quantification of aggregate formation in living cells in an inducible HD cell model.ResultsRat pheochromocytoma (PC12) cells containing a stably integrated, doxycycline-inducible, eGFP-tagged N-terminal human Htt fragment with an expanded polyQ domain were used to analyse gene expression changes at different stages of mutant Htt aggregation. At earliest time points after doxycycline induction no detectable aggregates and few changes in gene expression were observed. Aggregates started to appear at intermediate time points. Aggregate formation and subsequent enlargement of aggregates coincided with a rapid increase in the number of differentially expressed (DE) genes. The increase in number of large aggregates coincided with a decrease in the number of smaller aggregates whereas the transcription profile reverted towards the profile observed before mutant Htt induction. Cluster-based analysis of the 2,176 differentially expressed genes revealed fourteen distinct clusters responding differently over time. Functional enrichment analysis of the two major gene clusters revealed that genes in the up-regulated cluster were mainly involved in metabolic (antioxidant activity and cellular ketone metabolic processes) and genes in the down-regulated cluster in developmental processes, respectively. Promoter-based analysis of the identified gene clusters resulted in identification of a transcription factor network of which several previously have been linked to HD.ConclusionsWe demonstrate a time-resolved relationship between Htt aggregation and changes in the transcriptional profile. We identified two major gene clusters showing involvement of (i) mitochondrial dysfunction and (ii) developmental processes implying cellular homeostasis defects. We identified novel and known HD-linked transcription factors and show their interaction with known and predicted regulatory proteins. Our data provide a novel resource for hypothesis building on the role of transcriptional key regulators in early stages of HD and possibly other polyQ-dependent diseases.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3745-z) contains supplementary material, which is available to authorized users.

Heat shock promotes inclusion body formation of mutant huntingtin (mHtt) and alleviates mHtt-induced transcription factor dysfunction

“…An important cause of the neurotoxicity of disease proteins implicated in ND is the anomalous interactions with many metastable regulatory proteins causing multifactorial toxicity and collapse of essential cellular functions (33,75). In HD, there is widespread transcription dysfunction (32)(33)(34). Herein, we show that although HSF1-mediated induction of HSPs guides diffuse mHtt to form IBs and improves cell fitness, there is a negative feedback loop, namely, the expression of diffuse mHtt limits and constrains the activity of HSF1.…”

“…Transcription dysregulation is an important pathogenic mechanism in HD, and major changes in gene expression have been detected in postmortem HD brains and experimental model systems (32)(33)(34). Given the well-documented role of HSF1 as a driver of the HSP-dependent PQC system and its dysfunction in many model systems of aging (6 -8, 11, 14, 17, 35), we asked if expression of mHtt may in turn affect the regulation and function of HSF1.…”

Bioinformatic analysis of microRNA expression in Huntington's disease

“…In total, 1,612 DEGs and 10 DEMs were identified. GO function (BP, CC, and MF) and biological pathway analysis of DEGs demonstrated the majority of genes were involved in some processes and pathways, such as signal transduction in BP ( 28 ), plasma membrane in CC ( 29 ), transcription factor activity in MF ( 30 ), and immune system in biological pathway ( 28 ). Changes in Ca 2+ signaling and/or transduction systems and misfolded protein-plasma membrane interactions affected HD initiation and progression as reported by Fan and Shrivastava ( 29 , 31 ).…”

Osmolytes dynamically regulate mutant Huntingtin aggregation and CREB function in Huntington’s disease cell models

“…This is coincident with the de-repression of cAMP-response element binding protein (CREB), heat shock factor 1 (HSF1), and nuclear factor κ light chain enhancer of activated B cells (NFκB) function, transcription factors implicated in memory formation, stress resistance and neuron survival 9 . This work adds to a growing stream of evidence that diffusible entities of disease proteins can drive pathogenesis, in part by binding to and quenching key regulatory proteins and the aggregation of disease proteins may represent a coping mechanism or consequence in disease states 2 , 6 , 7 , 10 .…”

“…drive pathogenesis, in part by binding to and quenching key regulatory proteins and the aggregation of disease proteins may represent a coping mechanism or consequence in disease states 2,6,7,10 .…”