Exploring Leukemic Stem Cells: From molecular screen to single-cell transcriptomics

Hematopoiesis is the biological process leading to the formation of all functional cells of the blood. This process of precise differentiation from a hematopoietic stem cell (HSC) to the effector cells, through distinct progenitor stages, is the result of a tight regulation.
Hematopoiesis is typically divided into three branches from the less differentiated cells: lymphoid, erythroid, and myeloid, and leads to the formation of cells responsible for our immune system, the transport of oxygen, and the maintenance of blood vessels integrity.
Acute Myeloid Leukemia (AML) is the consequence of malignant transformations along the myeloid branch. It is characterized by the accumulation of progenitors blocked in their differentiation, resulting in the absence of functional cells in the blood.
Despite the increased understanding of the diseases’ complexity, the best treatments available nowadays still lead to high rates of relapse, in part due to a small population of cells able to re-initiate the disease that has been characterized as Leukemic Stem Cells (LSC).
However, due to the high heterogeneity in AML resulting from its clonal evolution, their characterization and targeting remain intricate. Additionally, the balance between selfrenewal and differentiation of HSCs is orchestrated by the regulation of genomic expression which, in turn, is controlled by epigenetic processes regulating chromatin accessibility.
Proteins involved in this regulation, known as epigenetic factors, are often found mutated in myeloid malignancies and pre-leukemic stages, and play a critical role in LSC.
In this thesis, we explored LSCs along 2 axes: One looking at the impact of different epigenetic factors on their fitness to identify new targetable actors to affect LSCs’ survival. The other alleviates the heterogeneity of AML by looking at single-cell transcriptomics data to highlight subtype-specific characteristics of LSCs in genetically defined AML.
We designed an shRNA screen focusing on epigenetic and DNA/RNA binding factors to uncover new potential targets against LSC, centered on the role of epigenetic factors as regulators of hematopoietic differentiation. The disruption of PHF3 expression reduced the proliferation of AML cells and impaired the engraftment of the LSC enriched population promoting their differentiation. This highlights PHF3 as an interesting candidate to hit LSC.
On the other hand, we focused on distinct genetically defined AML subtypes to investigate LSCs’ characteristics through AML heterogeneity. We highlighted specific differentiation patterns within the different subtypes and a population of cells with higher LSC signature was associated with distinct changes in gene expression according to their subtypes.
Together, these data are contributing to the general understanding of LSC and contribute to the urgent need to identify new targets to affect them in order to prevent AML relapse in a subtype-specific manner considering the complexity of the disease.