Long Non-Coding RNA LINC00152 Regulates Self-Renewal of Leukemia Stem Cells and Induces Chemo-Resistance in Acute Myeloid Leukemia

Abstract

Relapse of acute myeloid leukemia (AML) has a very poor prognosis and remains a common cause of treatment failure in patients with this disease. AML relapse is partially driven by the chemoresistant nature of leukemia stem cells (LSCs), which remains poorly understood, and our study aimed at elucidating the underlying mechanism. Accumulating evidences show that long noncoding RNAs (lncRNAs) play a crucial role in AML development. Herein, the lncRNA, LINC00152, was identified to be highly expressed in CD34⁺ LSCs and found to regulate the self-renewal of LSCs derived from AML patients. Importantly, LINC00152 upregulation was correlated with the expression of 16 genes within a 17-gene LSC biomarker panel, which contributed to the accurate prediction of initial therapy resistance in AML. Knockdown of LINC00152 markedly increased the drug sensitivity of leukemia cells. Furthermore, LINC00152 expression was found to be correlated with poly (ADP-ribose) polymerase 1 (PARP1) expression in AML, whereas LINC00152 knockdown significantly decreased the expression of PARP1. Upregulation of LINC00152 or PARP1 was associated with poor prognosis in AML patients. Collectively, these data highlight the importance and contribution of LINC00152 in the regulation of self-renewal and chemoresistance of LSCs in AML.

Keywords: LINC00152; chemo-resistance; leukemia; leukemia stem cells; poly (ADP-ribose) polymerase 1.

Figure 1

LINC00152 expression is upregulated in leukemia stem cells (LSCs). (A) CD34⁺CD38⁻ and CD34⁻CD38⁺ cell subpopulations were sorted by flow cytometry from 15 acute myeloid leukemia (AML) patients. (B) Colony formation assay using sorted CD34⁺CD38⁻ and CD34⁻CD38⁺ cells was performed and the mean number of clone forming units was analyzed. Data are presented as the mean ± SEM of three independent experiments (***P < 0.001). (C) LINC00152 expression in CD34⁺CD38⁻ and CD34⁻CD38⁺ cells derived from five AML patients. Data are represented as the mean ± SD of three independent experiments (*P < 0.05). (D) Correlation between overall survival of AML patients and LINC00152 expression (based on a publicly available data set by gene expression profiling interactive analysis (***P < 0.001).

Figure 2

Correlation between LINC00152 expression and leukemia stem cell (LSC)-associated gene expression. LSC17 biomarker gene profile and LINC00152 expression were analyzed based on a publicly available data set (GSE76009) by gene expression profiling interactive analysis.

Figure 3

LINC00152 knockdown decreases the capacity of colony formation of LSCs. (A) LINC00152 expression in cells transfected with short hairpin RNAs (shCTRL or sh00152s) (*P < 0.05, ***P < 0.001). (B–D) Quantification of colony formation derived from three acute myeloid leukemia patients. Data are presented as the mean ± SEM of three independent experiments (*P < 0.05, **P < 0.01).

Figure 4

LINC00152 regulates chemoresistance of leukemia stem cells (LSCs) via PARP1. (A) Doxorubicin sensitivity assay after LINC00152 knockdown in K562 cells. (B) PARP1 mRNA level after LINC00152 knockdown compared with control acute myeloid leukemia (AML) cells (*P < 0.05, **P < 0.01). (C) PARP1 expression at the protein level after LINC00152 knockdown compared with control AML cells. (D) PARP1 expression in CD34⁺CD38⁻ and CD34⁻CD38⁺ cells derived from five AML patients. Data are represented as the mean ± SD of three independent experiments (**P < 0.01). (E) Expression of LINC00152 was correlated with that of PARP1 in AML based on a publicly available data set by gene expression profiling interactive analysis. (F) PARP1 expression in paired CD34⁺ cells vs. CD34⁻ cells (GSE30029, ***P < 0.001). (G) PARP1 expression in CD34⁺CD38⁻ vs. CD34⁻CD38⁺ cells (GSE760008, ***P < 0.001). (H) Correlation between overall survival of AML patients and PARP1 expression based on a publicly available data set (GSE76009) by gene expression profiling interactive analysis.

Figure 5

Both LINC00152 and PARP1 expression correlated with DNA damage repair in acute myeloid leukemia. High expression of LINC00152 and PARP1 individually enriched the genes associated with nucleotide-excision repair, preincision complex stabilization (A, B), nucleotide-excision repair, DNA duplex unwinding (C, D), and global genome nucleotide-excision repair (E, F).