Abstract 2008: The N6-methyladenine-long noncoding RNA axis promotes drug resistance through PI3k signaling in leukemia
Authors: Tan Yanhong , Zhou Changli , Bian Sicheng , Walter Wencke , Pang Jiuxia , Cheng Tao , Huang Gang , Hoermann Gregor , Tse William , Liu Shujun 
Published: March 2024

Disease recurrence characterized by drug resistance remains a major hurdle to the successful cancer treatment. Long noncoding RNAs (lncRNAs) and RNA N⁶-methyladenosine (m6A) have been linked to cancer recurrence. However, if and how lncRNAs and m6A coordinately determine drug resistance in tyrosine kinase (TK)-driven cancers are still unclear. We hypothesize that upon exposure to TK inhibitors (TKI), the dynamic m6A methylation epitransciptomically allows a set of proliferation/anti-apoptosis-relevant lncRNAs bearing m6A motifs to be rapidly upregulated, thus facilitating a subpopulation of cancer cells to evade TKI killing. By performing transcriptomic and epitransciptomic profiling in long-term TKI (nilotinib)-deprived leukemia resistant cells, we show that many differentially expressed lncRNAs enrich m6A, and more lncRNAs tend to have higher m6A content in resistant cells. We further demonstrate a broad clinical relevance of our findings, showing that upregulation of specific top-ranked lncRNAs (e.g., SENCR, PROX1-AS1, LN892) in TKI-resistant cell lines also occurs in leukemia patients at the diagnostic stage, blast crisis phase or in those not-responding to TKI treatment compared to chronic phase or TKI responders, respectively. Some of the upregulated lncRNAs in leukemia patients pre- and post-TKI treatment predict unfavorable outcomes and are associated with shorter survival duration. Through proliferative and clonogenic assays, we demonstrate that knockdown of SENCR, PROX1-AS1 or LN892 impairs resistant cell growth and renders resistant cells sensitive to nilotinib-induced cell death. We further found that this lncRNA upregulation is attributed to FTO-dependent m6A hypomethylation that stabilizes lncRNA transcripts. Using ectopic expression or genetic/pharmacological inhibition, we demonstrate that lncRNA upregulation empowers resistant cell growth through an activated PI3K signaling as supported by overexpression of PI3K signaling mediators (e.g., ITGA2, F2R, COL6A1). Treatment with PI3K inhibitor alpelisib sensitizes TKI-resistant cells to TKI-induced cell death and reduces leukemia burden in mice via downregulation of F2R, ITGA2, and COL6A1. In conclusion, our findings add a new layer to the complexity of mechanisms regulating leukemia cell fate under TKI selection and raise the possibility that the m6A-regulated lncRNAs represents a new non-genetic factor to affect the development and maintenance of TKI resistance; our discoveries identify a promising therapeutic target, the m6A-lncRNAs axis, for specifically the most challenging patient subpopulations who are TKI non-responders/relapsed but do not carry the acquired mutations on top of BCR/ABL; our results also uncover a strong predictor, m6A-regulated lncRNA-PI3K axis, for poorer prognosis and failure in drug response which might be a pan-cancer mechanism.

Citation Format: Yanhong Tan, Changli Zhou, Sicheng Bian, Wencke Walter, Jiuxia Pang, Tao Cheng, Gang Huang, Gregor Hoermann, William Tse, Shujun Liu. The N6-methyladenine-long noncoding RNA axis promotes drug resistance through PI3k signaling in leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2008.