Fourneaux Camille, Racine Laëtitia, Koering Catherine, Dussurgey Sébastien, Vallin Elodie, Moussy Alice, Parmentier Romuald, Brunard Fanny, Stockholm Daniel, Modolo Laurent, Picard Franck, Gandrillon Olivier, Paldi Andras, Gonin-Giraud Sandrine
Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR5239, Université Claude Bernard Lyon 1, Lyon, France.
Ecole Pratique des Hautes Etudes, PSL Research University, Sorbonne Université, INSERM, CRSA, Paris, 75012, France.
BMC Biol. 2024 Mar 12;22(1):58. doi: 10.1186/s12915-024-01846-9.
Cell differentiation requires the integration of two opposite processes, a stabilizing cellular memory, especially at the transcriptional scale, and a burst of gene expression variability which follows the differentiation induction. Therefore, the actual capacity of a cell to undergo phenotypic change during a differentiation process relies upon a modification in this balance which favors change-inducing gene expression variability. However, there are no experimental data providing insight on how fast the transcriptomes of identical cells would diverge on the scale of the very first two cell divisions during the differentiation process.
In order to quantitatively address this question, we developed different experimental methods to recover the transcriptomes of related cells, after one and two divisions, while preserving the information about their lineage at the scale of a single cell division. We analyzed the transcriptomes of related cells from two differentiation biological systems (human CD34+ cells and T2EC chicken primary erythrocytic progenitors) using two different single-cell transcriptomics technologies (scRT-qPCR and scRNA-seq).
We identified that the gene transcription profiles of differentiating sister cells are more similar to each other than to those of non-related cells of the same type, sharing the same environment and undergoing similar biological processes. More importantly, we observed greater discrepancies between differentiating sister cells than between self-renewing sister cells. Furthermore, a progressive increase in this divergence from first generation to second generation was observed when comparing differentiating cousin cells to self renewing cousin cells. Our results are in favor of a gradual erasure of transcriptional memory during the differentiation process.
细胞分化需要整合两个相反的过程，一个是稳定的细胞记忆，特别是在转录水平上，另一个是在分化诱导后基因表达变异性的爆发。因此，细胞在分化过程中发生表型变化的实际能力取决于这种平衡的改变，这种改变有利于诱导变化的基因表达变异性。然而，目前尚无实验数据能够深入了解在分化过程的最初两个细胞分裂阶段，相同细胞的转录组在多大程度上会发生分化。
为了定量解决这个问题，我们开发了不同的实验方法，以在一次和两次分裂后恢复相关细胞的转录组，同时在单细胞分裂水平上保留其谱系信息。我们使用两种不同的单细胞转录组学技术（scRT-qPCR和scRNA-seq）分析了来自两个分化生物学系统（人类CD34+细胞和T2EC鸡原代红细胞祖细胞）的相关细胞的转录组。
我们发现，正在分化的姐妹细胞的基因转录谱彼此之间比与相同类型的非相关细胞更相似，它们共享相同的环境并经历相似的生物学过程。更重要的是，我们观察到正在分化的姐妹细胞之间的差异比自我更新的姐妹细胞之间的差异更大。此外，当比较正在分化的堂兄弟细胞与自我更新的堂兄弟细胞时，从第一代到第二代这种差异逐渐增加。我们的结果支持在分化过程中逐渐消除转录记忆的观点。
