RNA-seq analysis reveals significant transcriptome changes in huntingtin-null human neuroblastoma cells.
RNA-seq analysis reveals significant transcriptome changes in huntingtin-null human neuroblastoma cells.
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DOI：
10.1186/s12920-021-01022-w
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发表时间：
2021-07-02
影响因子：
2.7
通讯作者：
Wei J
中科院分区：
文献类型：
--
作者：
Bensalel J;Xu H;Lu ML;Capobianco E;Wei J
亨廷顿蛋白（Huntingtin，Htt）是亨廷顿病（Huntington's disease，HD）中基因突变的产物，亨廷顿病是一种致命的、常染色体显性遗传的神经退行性疾病。正常的Htt对于早期胚胎发生和中枢神经系统的发育是必不可少的。然而，Htt在成人组织中的作用不太明确。在最近有希望的临床试验中，正常和突变的Htt mRNA在HD患者中被敲除，迫切需要充分了解敲除/敲除Htt在成人组织中的分子后果。Htt是一种重要的转录调控因子。已在HD的多种细胞类型中使用RNA测序（RNA-Seq）对转录组变化进行了无偏倚研究，进一步证实转录失调是HD的中心致病机制。然而，缺乏对正常Htt的转录调控的直接理解。为了研究正常Htt的转录作用，我们首先使用CRISPR（成簇规则间隔短回文重复序列）-Cas9（CRISPR相关蛋白9）基因编辑方法敲除人神经母细胞瘤SH-SY 5 Y细胞系中的Htt。然后，我们对Htt缺失和野生型SH-SY 5 Y细胞进行RNA-seq分析，以探测由Htt缺失诱导的全局转录组变化。一般来说，Htt对基因转录具有广泛的影响。使用各种生物信息学工具对差异表达基因（DEG）进行功能分析，揭示了与细胞通讯和信号传导相关的通路中的不规则性，更具体地说，与神经元发育，神经传递和突触信号传导相关的通路中的不规则性。我们进一步研究了可能调节这些DEG的转录因子。与细胞发育相关的破坏途径相一致，我们表明，Htt无效细胞表现出比野生型细胞更慢的细胞增殖。最后，我们用定量RT-PCR验证了一些顶级DEGS。在Htt-无效细胞中广泛的转录组变化可能是由Htt介导的转录调控的丧失直接引起的，或者是由于基因调控网络中断的继发后果。因此，我们的研究提供了有价值的信息与Htt介导的转录相关的关键基因，并提高了我们的理解的分子机制的细胞功能的正常和突变的Htt。在线版本包含补充材料，可通过10.1186/s12920-021-01022-w获得。
Huntingtin (Htt) protein is the product of the gene mutated in Huntington’s disease (HD), a fatal, autosomal dominant, neurodegenerative disorder. Normal Htt is essential for early embryogenesis and the development of the central nervous system. However, the role of Htt in adult tissues is less defined. Following the recent promising clinical trial in which both normal and mutant Htt mRNA were knocked down in HD patients, there is an urgent need to fully understand the molecular consequences of knocking out/down Htt in adult tissues. Htt has been identified as an important transcriptional regulator. Unbiased investigations of transcriptome changes with RNA-sequencing (RNA-Seq) have been done in multiple cell types in HD, further confirming that transcriptional dysregulation is a central pathogenic mechanism in HD. However, there is lack of direct understanding of the transcriptional regulation by normal Htt. To investigate the transcriptional role of normal Htt, we first knocked out Htt in the human neuroblastoma SH-SY5Y cell line using the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 (CRISPR-associated protein 9) gene editing approach. We then performed RNA-seq analysis on Htt-null and wild type SH-SY5Y cells to probe the global transcriptome changes induced by Htt deletion. In general, Htt has a widespread effect on gene transcription. Functional analysis of the differentially expressed genes (DEGs) using various bioinformatic tools revealed irregularities in pathways related to cell communication and signaling, and more specifically those related to neuron development, neurotransmission and synaptic signaling. We further examined the transcription factors that may regulate these DEGs. Consistent with the disrupted pathways associated with cellular development, we showed that Htt-null cells exhibited slower cell proliferation than wild type cells. We finally validated some of the top DEGS with quantitative RT-PCR. The widespread transcriptome changes in Htt-null cells could be directly caused by the loss of Htt-mediated transcriptional regulation or due to the secondary consequences of disruption in the gene regulatory network. Our study therefore provides valuable information about key genes associated with Htt-mediated transcription and improves our understanding of the molecular mechanisms underlying the cellular functions of normal and mutant Htt. The online version contains supplementary material available at 10.1186/s12920-021-01022-w.
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影响因子：
25
作者：
Lo Sardo, Valentina;Zuccato, Chiara;Cattaneo, Elena
通讯作者：
Cattaneo, Elena
DOI：
10.1093/brain/awr333
发表时间：
2012-04
期刊：
Brain : a journal of neurology
影响因子：
--
作者：
Grondin R;Kaytor MD;Ai Y;Nelson PT;Thakker DR;Heisel J;Weatherspoon MR;Blum JL;Burright EN;Zhang Z;Kaemmerer WF
通讯作者：
Kaemmerer WF
DOI：
10.1111/j.1460-9568.2010.07215.x
发表时间：
2010-06
期刊：
The European journal of neuroscience
影响因子：
--
作者：
Leon R;Bhagavatula N;Ulukpo O;McCollum M;Wei J
通讯作者：
Wei J
影响因子：
4.5
作者：
Dietrich P;Johnson IM;Alli S;Dragatsis I
通讯作者：
Dragatsis I
影响因子：
4.7
作者：
Gourfinkel-An, I;Parain, K;Hirsch, EC
通讯作者：
Hirsch, EC