RNA binding protein-directed control of leukemic stem cell evolution and function

Abstract

Strict control over hematopoietic stem cell decision making is essential for healthy life-long blood production and underpins the origins of hematopoietic diseases. Acute myeloid leukemia (AML) in particular is a devastating hematopoietic malignancy that arises from the clonal evolution of disease-initiating primitive cells which acquire compounding genetic changes over time and culminate in the generation of leukemic stem cells (LSCs). Understanding the molecular underpinnings of these driver cells throughout their development will be instrumental in the interception of leukemia, the enabling of effective treatment of pre-leukemic conditions, as well as the development of strategies to target frank AML disease. To this point, a number of precancerous myeloid disorders and age-related alterations are proving as instructive models to gain insights into the initiation of LSCs. Here, we explore this myeloid dysregulation at the level of post-transcriptional control, where RNA-binding proteins (RBPs) function as core effectors. Through regulating the interplay of a myriad of RNA metabolic processes, RBPs orchestrate transcript fates to govern gene expression in health and disease. We describe the expanding appreciation of the role of RBPs and their post-transcriptional networks in sustaining healthy hematopoiesis and their dysregulation in the pathogenesis of clonal myeloid disorders and AML, with a particular emphasis on findings described in human stem cells. Lastly, we discuss key breakthroughs that highlight RBPs and post-transcriptional control as actionable targets for precision therapy of AML.

Figure 1

Dynamic regulation of RNA across leukemic transformation. (A) Healthy hematopoietic stem cells are defined by their ability to balance their capacity for self‐renewal and differentiation, enabling sustained lifelong blood production. The acquisition of germline mutations, or somatic mutations with age, leads to a variety of blood disorders that are characterized by increasingly clonal and defective hematopoiesis. As mutated hematopoietic stem or progenitor cells clones continue expanding and acquiring additional mutations, they ultimately give rise to leukemic stem cells, resulting in the initiation of frank leukemia. (B) Messenger RNA (mRNA) can be regulated by a variety of processes to ultimately govern whether it is translated into a protein and what protein isoform is produced. The spliceosome and other splicing factors splice pre‐mRNA to generate mRNA isoforms, that are then acted upon by a variety of RNA‐binding proteins to regulate its stability, localization, and transport to either ensure or prevent its translation. (C) RNA processes are highly dynamic across leukemic transformation, and often display broad patterns of change as healthy hematopoiesis gives way to leukemia, an example being generally increasing isoform diversity. Even so, particularly with translation rates in pre‐leukemic states, there exists somewhat paradoxical directions of change, highlighting the possibility of post‐transcriptional regulatory heterogeneity within a transformation state.

Figure 2

Post‐transcriptional enforcement of healthy hematopoietic stem cell function. Healthy HSCs rely on tightly controlled protein synthesis, where global protein synthesis rates are low compared to more mature cell populations, and transcript expression is tightly controlled. (A) Binding of regulatory RNA‐binding proteins (RBPs) can often de‐stabilize messenger RNA (mRNAs) or impair their translation. Binding of microRNA‐RISC complexes can additionally degrade mRNAs to decrease their expression. In addition, regulatory RBPs can impair the biogenesis of microRNAs, to inhibit their capacity to degrade their mRNA targets. (B) Alternative splicing and certain splice factors can also maintain the expression of specific protein isoforms that are tied to maintaining HSC functionality. Exemplifying pathway cross‐talk, alternative splicing can remove microRNA binding sites allowing transcripts to escape repression and be expressed as described in (A). (C) m6A writers and readers can deposit or act on m6A marks to enforce or impair translation in a highly context‐dependent manner. This regulation can often be linked to HSC fate decisions, where protein expression is regulated to either enable proper differentiation or promote maintenance of the HSC state, highlighting the dynamic nature of m6A effects. (D) 4E‐BPs remain hypo‐phosphorylated to maintain reduced translation rates in HSCs.

Figure 3

Post‐transcriptional dysregulation in leukemia primed states. Malignant states that predispose patients to leukemia are often acquired through somatic or germline mutations. These ultimately affect what messenger RNA (mRNA) or protein isoform is translated and expressed. (A) Similar to the healthy system, regulatory RNA‐binding proteins (RBPs) can affect mRNA translation to promote malignancy. (B) MDS is characterized by a uniquely high incidence of splice factor mutations, such as in SRSF2, U2AF1, SF3B1, and ZRSR2. The resulting splicing alterations can result in frameshifting events or inclusion of poison exons which can both result in premature stop codons and mRNA degradation through nonsense‐mediated decay. Alternatively, the inclusion of exons in‐frame can lead to pathogenic gain‐of‐function events. (C) Pseudouridine (Ψ) modified 5′‐tRNA fragments containing a 5′‐oligoguanine (mTOGs) interfere with cap‐complex assembly reducing translation. (D) Ribosomapathies generate mutated ribosomal proteins or impair ribosome biogenesis, resulting in the decreased translation of key transcripts. Similar effects can be achieved through somatic mutations of genes that similarly impair ribosome function.

Figure 4

Post‐transcriptional enforcement of the AML state and leukemic stem cell function. Post‐transcriptional regulation plays an important role in leukemia and LSCs by dually enforcing the expression of pro‐leukemogenic transcripts, while repressing transcripts that are anti‐leukemic. (A) Regulatory RNA‐binding proteins (RBP) binding, or the loss of microRNAs potentially mediated through regulatory RBP activity, can drive the expression of leukemic transcripts. (B) Alternative splicing can enable or enforce the expression of pathogenic transcript isoforms or cause nonsense mediated decay events and thus the loss of expression of certain isoforms. As an example of pathway crosstalk, altered splicing of base editors can result in new gain‐of‐function isoforms and subsequent pathogenic edits. (C) RNA modification readers, writers and erasers, or base editors, can similarly drive leukemia in a highly context‐specific manner through enforcing or impairing gene expression, where the nature of their specific targets is highly informative to their function. (D) The diverse modes of post‐transcriptional regulation described above all feed into translational regulation to enable leukemogenesis and LSC function.