Page 30 - Haematologica May 2022

D. Papaioannou et al.
Prognostic significance of recurrent long non-coding RNA variants in acute myeloid leukemia
We proceeded to examine the associations of the lncRNA variants with the clinical outcome of younger patients with CN-AML. Of the variants tested, 41 associated with more than one outcome endpoint (DFS, OS and/or EFS; Online Supplementary Table S3) above a threshold level of signifi- cance (P<0.05). There was no association between the pres- ence of lncRNA variants and complete remission rates in our cohort.
Among the variants that showed significant association with clinical outcome in our dataset were a C-to-T variant in the lncRNA RP5-1074L1.4 (RP5-1074L1.4varT), and SNHG15varT, a C-to-T variant in the lncRNA SNHG15.
In patients with detectable RP5-1074L1.4 expression (n=243), the presence of the RP5-1074L1.4varT was found in 156 (64%) of them. Patients with the RP5-1074L1.4varT had longer DFS (P<0.001) than patients with wild-type RP5-1074L1.4 (RP5-1074L1.4wt); 5 years after diagnosis 44% of the RP5-1074L1.4varT patients were alive and leukemia-free in contrast to only 26% of those with RP5- 1074L1.4wt. RP5-1074L1.4varT was also associated with longer EFS (P<0.001; 5-year rates: 38% vs. 21%) and showed a trend for longer OS (P=0.09; 5-year rates: 43% vs. 34%; Figures 2 A to C; Online Supplementary Table S4).
Among patients who expressed the SNHG15 lncRNA (n=306), SNHG15varT was detected in 78% of them (n=239). Patients who expressed the SNHG15varT had longer DFS (P=0.04; 5-year rates: 37% vs. 22%) than patients who expressed the SNHG15wt. SNHG15varT expressers also had longer EFS (P=0.04; 5-year rates: 31% vs. 19%) and a trend for longer OS (P=0.07; 5-year rates: 41% vs. 32%) compared with SNHG15wt expressers (Figures 3A to C; Online Supplementary Table S5).
Finally, we examined whether genetic variants were detectable in the set of 24 lncRNA, whose expression levels were previously shown to associate with the clinical out- come of younger adults with CN-AML.30 We found seven such variants in three of the prognostic lncRNA (annotated in bold lettering in the Online Supplementary Table S1). A guanosine (G)-to-C variant in the lncRNA AL122127.25 (AL122127.25varC) was the only one that associated with patient outcome. AL122127.25varC was detected in 72 of the 257 patients who expressed the AL122127.25 lncRNA (i.e., 28% of the AL122127.25 expressers). The presence of AL122127.25varC significantly associated with shorter DFS (P=0.01; 5-year rates: 17% vs. 35%), OS (P=0.01; 5-year rates: 22% vs. 40%) and EFS (P=0.002; 5-year rates: 12% vs. 30%; Online Supplementary Figures S1A to C; Online Supplementary Table S6) in younger adult CN-AML patients. Notably, the presence of AL122127.25varC had no impact on the expression levels of the AL122127.25 transcript, when compared to the AL122127.25wt (Online Supplementary Figure S2).
Associations of long non-coding RNA variants with pretreatment clinical and molecular characteristics
Next, we examined potential associations of RP5- 1074L1.4varT, SNHG15varT and AL122127.25varC with pretreatment clinical characteristics and prognostic molecu- lar features of younger adult CN-AML patients. Overall, there were only minor differences in these features between variant and wild-type lncRNA expressers. Patients expressing the RP5-1074L1.4varT were more likely to har- bor tyrosine kinase domain mutations of the FLT3 gene
Table 1. Multivariable analyses of outcome in younger adult patients with cytogenetically normal acute myeloid leukemia by expression of the C-to-T variant of the RP5-1074L1.4 long non-coding RNA (IncRNA) (RP5-1074L1.4varT) versus the wild-type lncRNA (RP5-1074L1.4wt).
DFS
EFS
HR P
(95% CI)
0.54 <0.001 (0.40-0.75)
2.16 <0.001 (1.54-3.02)
1.90 0.006 (1.20-3.02)
- -
0.36 0.001 (0.21-0.61)
0.41 <0.001 (0.28-0.58)
Variables in final models HR (95% CI)
P
RP5-1074L1.4, varT vs. wild-type
FLT3-ITD,
present vs. absent
0.54 <0.001 (0.37-0.77)
2.29 <0.001 (1.59-3.30)
WT1, 1.85 mutated vs. wild-type (1.04-3.27)
MN1 expression, 1.55 high vs. low (1.07-2.24)
CEBPA, - double-mutated vs. wild-type
NPM1, - mutated vs. wild-type
0.04 0.02 - -
DFS: disease-free survival; EFS: event-free survival; FLT3-ITD: internal tandem duplica- tion of the FLT3 gene; HR: hazard ratio; CI: confidence intervals; varT: C-to-T variant; vs.: versus. NOTE: Hazard ratios greater than (less than) 1.0 indicate higher (lower) risk for relapse or death (disease-free survival) or death (overall survival) or for failure to achieve complete remission,relapse or death (event-free survival) for the first catego- ry listed for the categorical variables.Variables considered for model inclusion were: RP5-1074L1.4 (varT vs. wild-type), age (as a continuous variable, in 10-year incre- ments), sex (male vs. female), race (white vs. non-white), white blood cell count (as a continuous variable, in 50-unit increments), hemoglobin (as a continuous variable, in 1-unit increments),platelet count (as a continuous variable,in 50-unit increments), extramedullary involvement (present vs. absent), ASXL1 mutations (mutated vs. wild-type), CEBPA mutations (double-mutated vs. single-mutated or wild-type), DNMT3A mutations (mutated vs. wild-type), FLT3-ITD (present vs. absent), FLT3-TKD (present vs. absent), IDH1 mutations (mutated vs. wild-type), IDH2 mutations (mutat- ed vs. wild-type), NPM1 mutations (mutated vs. wild-type), RUNX1 mutations (mutat- ed vs. wild-type), TET2 mutations (mutated vs. wild-type), WT1 mutations (mutated vs. wild-type), ERG expression levels (high vs. low), BAALC expression levels (high vs. low),MN1 expression levels (high vs. low),miR-181a expression levels (high vs. low), miR-3151 expression (expressed vs. not expressed), and miR-155 expression levels (high vs. low).
(FLT3-TKD) than patients who expressed the RP5- 1074L1.4wt (P=0.03; 12% vs. 4%; Online Supplementary Table S7). Patients expressing the SNHG15varT were older (P=0.03), more likely to be Caucasian (P=0.02) and more likely to have low expression of the MN1 gene (P=0.05; Online Supplementary Table S8) than SNHG15wt expressers. With regard to the lncRNA AL122127.25, there were no sig- nificant differences in the clinical features or frequencies of prognostic gene mutations or gene expression between AL122127.25varC and AL122127.25wt expressers (Online Supplementary Table S9).
Multivariable analyses
In order to examine prognostic significance of the detect- ed lncRNA variants in the context of other established clin- ical and molecular prognostic markers, we constructed mul- tivariable models.
Expression of RP5-1074L1.4varT was a significant marker for longer DFS (hazard ratio [HR]: 0.54; P<0.001) and longer EFS (HR: 0.54; P<0.001) after adjusting for other covariates (Table 1). Expression of SNHG15varT significantly associat- ed with longer DFS (HR: 0.63; P=0.02), longer OS (HR: 0.63; P=0.008) and longer EFS (HR: 0.68; P=0.02) after adjusting for other variables for each outcome endpoint (Table 2). Finally, expression of the AL122127.25varC was an inde- pendent marker of shorter OS (HR: 1.57; P=0.009) and shorter EFS (HR: 1.59; P=0.004) after adjusting for other covariates (Online Supplementary Table S10).
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haematologica | 2022; 107(5)