In the complex landscape of genetic regulation, the role of RNA goes far beyond its classical function as a mere messenger between DNA and protein synthesis. Recent research has illuminated the multifaceted roles of non-coding RNAs (ncRNAs) in transcription regulation, chromatin modulation and genome organization during tissue development as well as disease pathology [1,2]. Our study delves into this intricate world, uncovering the pivotal roles of chromatin-associated small non-coding RNAs in the maintenance and propagation of acute myeloid leukemia (AML).

Why We Worked On This

AML is a devastating hematological malignancy characterized by the uncontrolled proliferation of myeloid precursor cells [3]. It largely affects the adults and generally has a dismal outcome. Despite advancements in our understanding of the dysregulated gene network driving AML, the regulatory roles of RNA in this context remain largely unexplored. This knowledge gap inspired us to explore the RNA-chromatin interactome in leukemia cells. We aimed to identify key ncRNAs that interact with chromatin and unravel their potential roles in leukemia biology, with the hope of uncovering novel therapeutic targets.

How We Did It

To map the landscape of RNA-chromatin interactions in AML, we employed a cutting-edge technique known as in situ mapping of RNA-genome interactome (iMARGI) [4,5]. This method allowed us to capture and sequence RNA-DNA interaction pairs, providing a comprehensive view of the RNA species associated with chromatin. Our analysis was conducted on MV4-11 cells, a representative AML cell line, and involved generating and sequencing over one billion paired-end reads, resulting in the identification of approximately 52 million valid RNA-chromatin interactions.

What We Found

Our study revealed that protein-coding mRNAs and long non-coding RNAs (lncRNAs) predominantly interact with chromatin in cis, suggesting their involvement in transcriptional regulation at their sites of origin. In contrast, small ncRNAs, particularly small nucleolar RNAs (snoRNAs) and small nuclear RNAs (snRNAs), exhibited a high frequency of trans-interactions with chromatin, indicating specific roles in chromatin modulation beyond their traditional functions.

Among the chromatin-associated snoRNAs, SNORD118 and SNORD3A were captured for further analysis due to their widespread and predominant chromatin association in trans (Figure 1). The two snoRNAs were actively transcribed in multiple human leukemia cell lines, upregulated upon leukemia induction and reduced during myeloid differentiation. More interestingly, SNORD118 was significantly enriched in leukemia stem cells. Functional assays demonstrated that suppression of SNORD118 and SNORD3A impaired leukemia cell proliferation and colony-forming capacity in a number of AML cell line models and primary patient samples, whilst their loss had mild effects on healthy hematopoietic stem and progenitor cells (HSPCs), highlighting their essential role in leukemia maintenance.

Figure 1. Identification of two chromatin-associated snoRNAs in AML maintenance. (Created with BioRender.com)

What Our Work Means

The discovery of SNORD118 and SNORD3A as critical mediators of leukemia maintenance suggests new targets of AML intervention. In addition, these two snoRNAs have also been implicated in the propagation of breast cancer and lung cancer cells in vitro and in vivo [6], highlighting a potential general vulnerability in a broad spectrum of tumors. Our study revealed that unlike other snoRNAs, SNORD118 and SNORD3A function independently of the classical snoRNP complex and their chromatin association correlates with specific chromatin modification states. This unique chromatin-related mechanism may account for their functional importance in sustaining AML cells.

Our findings uncovered that inhibiting either of the two snoRNAs could selectively disrupt leukemia cell propagation while sparing healthy hematopoietic stem cells. This selective impact underscores the therapeutic promise of targeting specific ncRNAs in cancer treatment. However, further research is needed to elucidate the detailed molecular mechanisms by which SNORD118 and SNORD3A regulate chromatin and contribute to leukemia pathogenesis. Additionally, developing specific molecules or chemicals against these snoRNAs could pave the way for novel AML therapies.

Conclusion

Our study sheds light on the previously underappreciated roles of small ncRNAs in chromatin regulation and leukemia maintenance. These findings not only enhance our understanding of leukemia biology but also provide promising targets for future therapeutic development. As we continue to unravel the complexities of RNA-mediated regulation, we move closer to innovative treatments that could significantly improve outcomes for patients with AML.

 References

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