Loss of Heterozygosity in the Tumor DNA of De Novo Diagnosed Patients Is Associated with Poor Outcome for B-ALL but Not for T-ALL

Abstract

Despite the introduction of new technologies in molecular diagnostics, one should not underestimate the traditional routine methods for studying tumor DNA. Here we present the evidence that short tandem repeat (STR) profiling of tumor DNA relative to DNA from healthy cells might identify chromosomal aberrations affecting therapy outcome. Tumor STR profiles of 87 adult patients with de novo Ph-negative ALL (40 B-ALL, 43 T-ALL, 4 mixed phenotype acute leukemia (MPAL)) treated according to the "RALL-2016" regimen were analyzed. DNA of tumor cells was isolated from patient bone marrow samples taken at diagnosis. Control DNA samples were taken from the buccal swab or the blood of patients in complete remission. Overall survival (OS) analysis was used to assess the independent impact of the LOH as a risk factor. Of the 87 patients, 21 were found with LOH in various STR loci (24%). For B-ALL patients, LOH (except 12p LOH) was an independent risk factor (OS hazard ratio 3.89, log-rank p-value 0.0395). In contrast, for T-ALL patients, the OS hazard ratio was 0.59 (log-rank p-value 0.62). LOH in particular STR loci measured at the onset of the disease could be used as a prognostic factor for poor outcome in B-ALL, but not in T-ALL.

Keywords: acute lymphoblastic leukemia; chromosomal microarray (CMA); loss of heterozygosity (LOH); short tandem repeat (STR); uniparental disomy (UPD).

Figure 1

LOH patterns in STR profile of B-ALL patient 45 (a,b) molecular karyoview of CMA. The karyoview presents a diagram of all copy number variations (red bar for loss; blue bar for gain) and copy neutral LOH (purple bar). (LOH at 1q42, 10q26.3, 6q14, and 18q21.33 and disbalance at amelogenin X/amelogenin Y were verified by CMA as gains in areas including aberrant STR loci).

Figure 2

Kaplan–Meier survival curve for OS estimates according to the LOH status in tumor STR profile (LOH (except LOH 12p), red line; LOH 12p, green line; no LOH, blue line). Four patients with LOH 12p and additional LOH in several loci and five patients with unidentified LOH status were excluded from analysis.

Figure 3

Kaplan–Meier survival curve for OS estimates according to the LOH status in tumor STR profile for B-ALL (a) and T-ALL (b) patients. Patients 3, 4, 43, and 65 were excluded from the LOH group due to 12p LOH.