Cell Fate Safeguarding by the Mitochondrial Dehydrogenase IDH3 via linked Metabolism and Epigenetic Pathways in C. elegans.

未来的组织替代疗法需要特定的细胞类型来补充和修复患者的病变器官。例如，健康的神经细胞可以再生阿尔茨海默氏症患者的脑组织。新的健康细胞的一个有希望的来源是转换大量可用的细胞的身份，如星形胶质细胞或成纤维细胞。细胞类型转换是通过重新编程实现的，这需要特定转录因子的过度表达。然而，由于细胞命运保护机制的原因，转录因子在诱导重编程方面的效率通常受到限制。虽然关于细胞命运在发育过程中是如何确定的已经知道很多，但细胞的维护和保护机制还不完全清楚。然而，这对于改善未来再生医学应用的细胞重新编程是必不可少的。我们先前证明线虫是一种强大的模式生物，可以用来识别进化上保守的细胞保护机制(Müthel等人，2019年AgingCell；Hajduskova等人，2019年遗传学；Kolundzic等人，2018年DevCell；Seelk等人，2016年eLife；吐尔逊等人，2011年科学)。利用反向遗传学，我们现在发现保守的线粒体异柠檬酸脱氢酶IDH3是将生殖细胞重新编程为神经元的屏障。这种意想不到的障碍对新陈代谢至关重要，这引发了一个问题，即线粒体的扰动如何为细胞命运转换创造了通透性。我们的初步结果表明，IDH3缺失通过减少抑制性染色质而导致基因表达调节受损。然而，信号通路如何整合新陈代谢状态以引发表观遗传变化还不是很清楚。这项研究计划旨在破译分子途径，这些途径将新陈代谢和表观遗传学联系起来，以维持细胞状态并对抗重新编程。为了阐明相关的分子过程，我们正在将遗传学、细胞特异性转录组学(RNA-Seq)和染色质可及性分析(ATAC-Seq)与基于光谱分析的代谢物分析相结合。值得注意的是，我们还遇到了IDH3耗尽的非细胞自主影响，表明其他组织有助于生殖细胞命运的保护。关于非细胞自主效应的知识对未来的再生医学至关重要，因为它们在体外和体内可能具有相反的效应。因此，利用活体动物研究细胞保护和再编程可以揭示在完整组织的生理背景下影响细胞命运可塑性的关键细胞和跨组织途径。总体而言，关于代谢和表观基因表达调控的非细胞自主影响的知识是改善未来组织替代应用的重新编程的基础。

Prospective tissue replacement therapies require specific cell types to replenish and repair diseased organs of patients. For instance, healthy neuronal cells could regenerate brain tissues of Alzheimer’s patients. One promising source for new healthy cells is to convert the identity of abundantly available cells such as astrocytes or fibroblasts. Cell type conversion is achieved by reprogramming, which requires overexpression of specific transcription factors. However, transcription factors are usually restricted in their efficiency to induce reprogramming due to cell fate safeguarding mechanisms. While much is known about how cell fates are specified during development, cellular maintenance and safeguarding mechanisms are not fully understood. This, however, is essential to improve cellular reprogramming for future regenerative medicine applications. We previously demonstrated that the nematode C. elegans is a powerful model organism to identify evolutionarily conserved safeguarding mechanisms of cells (Müthel et al., 2019 AgingCell; Hajduskova et al., 2019 Genetics; Kolundzic et al., 2018 DevCell; Seelk et al., 2016 eLife; Tursun et al., 2011 Science). Using reverse genetics, we now identified the conserved mitochondrial isocitrate dehydrogenase IDH3 as a barrier for reprogramming germ cells into neurons. This unexpected barrier is critical for metabolism, raising the question of how perturbations in mitochondria create permissiveness for cell fate conversion. Our preliminary results indicate that IDH3 depletion causes impaired gene expression regulation by decreasing repressive chromatin. Yet, how signaling pathways integrate metabolic states to elicit epigenetic changes is not well understood. This research proposal aims at deciphering molecular pathways, which link metabolism and epigenetics to maintain cell states and counteract reprogramming. To elucidate relevant molecular processes, we are combining genetics, cell-specific transcriptomics (RNA-Seq), and chromatin accessibility assays (ATAC-Seq) with spectrometry-based analysis of metabolites. Strikingly, we also encountered non-cell-autonomous effects upon IDH3 depletion, indicating that other tissues contribute to germ cell fate safeguarding. Knowledge about non-cell-autonomous effects is essential for future regenerative medicine as they can have opposing effects in vitro vs. in vivo. Therefore, the use of living animals to study cellular safeguarding and reprogramming can reveal critical cellular and trans-tissue pathways that affect cell fate plasticity in the physiological context of intact tissues. Overall, knowledge about non-cell-autonomous effects of metabolic and epigenetic gene expression regulation is fundamental to improve reprogramming for future tissue replacement applications.