A Novel, Mitochondrial, Internal TRNA-derived RNA Fragment Possesses Clinical Utility As a Molecular Prognostic Biomarker in Chronic Lymphocytic Leukemia

Objectives: Chronic lymphocytic leukemia (CLL) is the most common leukemia among adults. The prognosis of CLL patients varies considerably. Transfer RNA-derived RNA fragments (tRFs) constitute a class of small non-coding RNA fragments excised from mature tRNAs and pre-tRNAs located in nuclei as well as in mitochondria. In this study, the clinical utility of i-tRF-Phe, a novel mitochondrial tRF, was investigated in CLL.

Design And Methods: Peripheral blood mononuclear cells (PBMCs) were isolated from 91 CLL patients and 43 non-leukemic controls. Total RNA was isolated from each sample, polyadenylated at the 3' end and reversely transcribed. An in-house developed real-time quantitative PCR assay was developed and applied, and the results were biostatistically analyzed. For the normalization of the i-tRF-Phe expression levels, the expression of a small nucleolar RNA (RNU48) was used as reference.

Results: Mann-Whitney U test showed that i-tRF-Phe can distinguish between CLL samples and normal controls (p < 0.001). As determined by Kaplan-Meier survival analysis, overexpression of i-tRF-Phe was related to poor overall survival of the CLL patients (p < 0.001). Univariate bootstrap Cox regression analysis exhibited a higher hazard ratio of 7.95 (95% CI = 2.37-26.72, p < 0.001) for patients with positive i-tRF-Phe expression status. Multivariate bootstrap Cox regression analysis showed that the prognostic value of this tRF is independent of clinical stage, mutational status of the immunoglobulin heavy chain variable (IGHV) genetic locus, and CD38 expression status (p = 0.010).

Conclusions: Our results show that i-tRF-Phe can serve as a molecular biomarker of poor prognosis in CLL, alongside with the existing factors for CLL prognosis.