The long noncoding RNA, treRNA, decreases DNA damage and is associated with poor response to chemotherapy in chronic lymphocytic leukemia.

Cecelia R Miller,Thomas J Kipps,Timothy L Chen,Deepa Sampath,Laura Z Rassenti,James S Blachly,Michael R Grever,Amy Lehman,David M Lucas,Chaomei Liu,Sydney Fobare,Kevin R Coombes,Martin S Tallman,Xiaoli Zhang,Ian W Flinn,Amy S Ruppert,Erin K Hertlein

doi:10.18632/oncotarget.15401

Abstract

The study of long noncoding RNAs (lncRNAs) is an emerging area of cancer research, in part due to their ability to serve as disease biomarkers. However, few studies have investigated lncRNAs in chronic lymphocytic leukemia (CLL). We have identified one particular lncRNA, treRNA, which is overexpressed in CLL B-cells. We measured transcript expression in 144 CLL patient samples and separated samples into high or low expression of treRNA relative to the overall median. We found that high expression of treRNA is significantly associated with shorter time to treatment. High treRNA also correlates with poor prognostic indicators such as unmutated IGHV and high ZAP70 protein expression. We validated these initial findings in samples collected in a clinical trial comparing the nucleoside analog fludarabine alone or in combination with the alkylating agent cyclophosphamide in untreated CLL samples collected prior to starting therapy (E2997). High expression of treRNA was independently prognostic for shorter progression free survival in patients receiving fludarabine plus cyclophosphamide. Given these results, in order to study the role of treRNA in DNA damage response we generated a model cell line system where treRNA was over-expressed in the human B-CLL cell line OSU-CLL. Relative to the vector control line, there was less cell death in OSU-CLL over-expressing treRNA after exposure to fludarabine and mafosfamide, due in part to a reduction in DNA damage. Therefore, we suggest that treRNA is a novel biomarker in CLL associated with aggressive disease and poor response to chemotherapy through enhanced protection against cytotoxic mediated DNA damage.

Highlights

Chronic lymphocytic leukemia (CLL) is a B-cell malignancy with a heterogeneous clinical course
We first sought to explore if long noncoding RNAs (lncRNAs) are differentially expressed in CLL by comparing pooled RNA isolated from CLL B-cells to pooled RNA from healthy donor peripheral blood B-cells, with and without stimulation with CD40 ligand
While validating differentially expressed lncRNA identified by microarray, we narrowed our interest to two lncRNAs, the role for a particular lncRNA (treRNA) and ENST00000413901, due to their variable expression in CLL patients and association with IGHV mutational status

Summary

INTRODUCTION

Chronic lymphocytic leukemia (CLL) is a B-cell malignancy with a heterogeneous clinical course. While some patients have indolent disease that may not require therapy for years, others progress quite rapidly Biomarkers such as unmutated IGHV, ZAP70 expression, and cytogenetic deletion of 17p or 11q have been identified as independent markers for aggressive disease [1,2,3,4]. Several miRs have been shown to play critical biological roles in CLL, in cell signaling. In CLL, we found high expression of treRNA was associated with poor response to chemotherapy independent of other variables, and suggest that treRNA may serve as a valuable prognostic factor in this disease. Using a CLL cell line model we show that over-expression of treRNA results in decreased DNA damage caused by exposure to chemotherapeutic agents, likely contributing to the impaired response and decreased clinical benefit observed in patients receiving these agents

RESULTS

DISCUSSION

MATERIALS AND METHODS