Abstract 2455: The long non-coding RNA (lncRNA) DANCR in acute myeloid leukemia (AML) stem cells (LSC)
Authors: Bill Marius , Karunasiri Malith , Kohlschmidt Jessica , Walker Allison E. , Brannan Zachary , Volinia Stefano , Bloomfield Clara D. , Garzon Ramiro , Dorrance Adrienne M. 
Published: August 2018

Introduction: Prognosis for AML patients (pts) is inadequate. Therapeutic strategies are needed to target not only bulk blasts but also the distinct LSCs, which are more resistant to chemotherapy & cause relapse. lncRNAs are non-coding RNA transcripts longer than 200 nucleotides that regulate cellular processes. A functional role in LSCs has yet to be elucidated.

Methods: We derived a LSC-specific lncRNA profile using whole transcriptome sequencing (RNA-seq) data of 377 pts (&lt;60 years) with cytogenetically normal (CN) AML. These data were correlated with a 'core enriched' (CE) gene expression signature representing 44 genes deregulated in LSCs (Eppert, Nat.Med. 2011). DANCR expression in the LSC-enriched compartment was validated using qRT-PCR. Transferrin/antibody conjugated nanoparticle (NP) knock down (KD) was used as an efficient & less toxic avenue to deliver siRNA against DANCR or scramble (SCR) in vitro & in vivo. LSC features (self-renewal, quiescence, engraftment) were analyzed & frequency determined in 3 primary AML samples and a CN-AML (Flt3ITD/WT/MllPTD/WT) mouse model.

Results: 161 lncRNAs were consistently deregulated in CEhigh pts with a p&lt;.001 & a correlation coefficient &gt;.5 (Spearmen correlation test). We chose DANCR to further analyze because it was among the top lncRNAs upregulated in CEhigh pts, is highly conserved between human & mouse, & was previously shown to have a role in promoting stemness in hepatocellular carcinoma (Yuan, Hepatology 2016). We confirmed that DANCR expression was significantly higher in functionally validated LSC enriched populations (p=.05). To assess the role in self-renewal, we KD DANCR in pts cells & found a decrease in colony numbers after replating (average decrease vs SCR: 38.9%, p=.03). Using membrane labeling assays, we found a decrease of quiescent cells after DANCR KD (average decrease: 36.1%, p=.04). Long term colony-initiating cell cultures were performed to determine the LSC frequency & we found significant decreases in the number of LSCs in primary pts samples after DANCR KD (average decrease of LSC frequency: 79.2%, p=.001). Mice transplanted with murine AML cells (CD45.2+) were treated with NP (n=3 per group) for 5 days (d). 2d later, bone marrow was harvested & retransplantated (Tx) using limiting dilutions (2x106, 1x106, 5x105) into irradiated BoyJ (CD45.1+) recipients (n=30). 14d post-Tx, anti-Dancr recipient mice showed a lower engraftment (CD45.2/CD45.1: 37% vs 47%, p=.03) and also a concomitant improvement in survival (p&lt;.001).

Conclusion: We show for the first time that LSCs have a distinct lncRNA profile. Among the highly expressed lncRNAs associated with LSCs we identified & validated DANCR. Our data show that DANCR has an impact on LSC function (self-renewal, quiescence, engraftment) & regulates LSC frequency. DANCR is the first lncRNA shown to have a functional role in LSCs & represents a novel target for AML treatment.

Citation Format: Marius Bill, Malith Karunasiri, Jessica Kohlschmidt, Allison E. Walker, Zachary Brannan, Stefano Volinia, Clara D. Bloomfield, Ramiro Garzon, Adrienne M. Dorrance. The long non-coding RNA (lncRNA) DANCR in acute myeloid leukemia (AML) stem cells (LSC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2455.