CRISPR-Cas9 技術於粒線體基因編輯之應用與對細胞功能之影響

Abstract

粒線體對於細胞進行能量代謝及維持動態恆定而言至關重要，當粒線體基因突變可能導致粒線體功能缺失，甚至引發嚴重疾病。粒線體基因病變與修復機制的研究具有高度挑戰性，而其仰賴於粒線體基因編輯工具的開發。過去有研究團隊嘗試利用限制酶、人工合成之DNA內切酶 (如:ZFN或TALENs)剔除突變之粒線體基因。近年來由於CRISPR-Cas9技術在目標基因位點設計及基因編輯之方便性等優勢下興起，此技術亦有開發於粒線體基因編輯之潛力，然而目前已知對於輸送嚮導RNA (guide RNA)至粒線體之細胞機制的研究並不深入。在這篇研究中，我們對Cas9蛋白以及嚮導RNA分別修飾粒線體標的序列(mitochondria targeting sequence; MTS)，促使其有效率的進入粒線體中。我們在高解析度共軛焦顯微鏡下證實mito-Cas9能進入粒線體內。藉由反轉錄PCR分析，我們在粒線體萃取中發現有增量之mito-sgRNA。然而在開發應用於粒線體基因編輯之Cas9系統(mito-Cas9 system)時，我們發現在HeLa細胞中表現mito-Cas9會造成細胞毒性而導致細胞凋亡，其中存活的細胞則有關閉mito-Cas9表現之現象，且輸送mito-sgRNA至細胞中會造成粒線體基因數量減少。為了建立一套完善的基因編輯系統，我們致力對mito-Cas9的表達時間與強度進行優化以降低其造成的粒線體壓力。這套mito-Cas9系統的開發可望應用於粒線體之基因體研究以及粒線體基因病變之治療。

Mitochondria are essential organelles in eukaryotic cells, indispensable for energy production, metabolisms and homeostasis. Mutations in mitochondrial genome (mtDNA) are highly disruptive to mitochondrial functions and cause devastating diseases. The research of mtDNA repair and mutation pathogenicity is challenging, and the lack of good genetic tools is one of the main reasons. Genetic editing of mtDNA is not a new idea and has been demonstrated by using restriction enzymes and programmable nucleases such as Zinc-finger nucleases, Transcription activator-like effector nucleases and more recently CRISPR-Cas9. Each technique has its strengths and limitations, and this work focuses on CRISPR-Cas9 system for mtDNA editing. RNA-guided DNA cleavage of Cas9 allows fast reprogramming of Cas9 target specificity. However, mitochondrial localization of the guide RNA requires specialized RNA import mechanisms that remain poorly understood. Here we describe the modifications of Cas9 protein (mito-Cas9) and guide RNA (mito-sgRNA) to achieve robust and specific mitochondrial localization. We present high-resolution confocal microscopic images of mitochondrial localization of mito-Cas9, which carries a novel mitochondrial targeting sequence. We also detected enrichment of mito-sgRNA, which carries a unique RNA hairpin, in the purified mitochondrial extract by reverse transcription-PCR using endogenous 5S rRNA as a benchmark. However, the reconstitution of mtDNA-targeting Cas9: guide RNA ribonucleoprotein complexes is difficult, owing to high cellular toxicity of mito-Cas9. The expression of mito-Cas9 alone in HeLa cell line by plasmid transfection induced mitochondrial fragmentation and cell death within two days. The surviving cells had completely silenced the expression of mito-Cas9 after three weeks. The transfection of in vitro transcribed mito-sgRNA caused reduced copies of mtDNA in HeLa cell line within one day. Strategies are needed to fine tune the expression level and timing of the mito-Cas9 system to avoid undesirable mitochondrial stress and enable unbiased detection of mtDNA cleavage. Successful establishment of a robust CRISPR-based mtDNA editing system will help advance mtDNA research and offer strategies for therapeutic correction of pathogenic mtDNA mutations.