Impact of Somatic Mutations on Outcome in Patients with MDS after Stem-Cell Transplantation

Background:

Allogeneic hematopoietic stem cell transplantation (HSCT) is the only curative therapy for patients with myelodysplastic syndromes (MDS), whose benefit, however, is frequently offset by accompanying mortality and morbidity, underscoring the importance of accurate prognostication before the therapeutic choice. For this purpose, several systems, such as the International Prognostic Scoring System (IPSS), are being successfully applied to clinics, and recent genome profiling studies indicate that molecular diagnostics can further improve the prediction. Nevertheless, existing systems are based on the observation from those patients who were untreated or only supportively treated and therefore, may not successfully be applied to the prognostication of the patients who are actually treated by HSCT.

Methods:

We analyzed patients with MDS (N = 719) from a cohort of Japan Marrow Donor Program (JMDP) who were treated by unrelated HSCT between 2006 and 2013. Peripheral blood DNA was subjected to targeted deep sequencing in 68 major driver genes for the detection of both somatic mutations and copy number variations (CNVs) with accurate determination of their allelic burdens.

Results:

The median age at HSCT and observation period were 53 years old (20-66) and 372 days (2-3001), respectively. At the diagnosis, 63, 203, 163 and 65 patients have low, intermediate-1, intermediate-2 and high risk classified on the basis of IPSS, respectively (IPSS data was not available for 250 patients). The median time from diagnosis to HSCT was 274 (9-10900) days.

Mutations were observed in 75% of the patients, of which TP53 was most frequently mutated (14.3%), followed by U2AF1 (13.2%), RUNX1 (12.2%), ASXL1 (11.0%) and DNMT3A(9.3%). The mean number of mutations was 2.1 per patient and the mean allelic burden was 23.4%. To evaluate karyotyping we combined metaphase cytogenetics and copy number variations using targeted sequencing data. Complex karyotype, chromosome 7 anomaly, deletion 5q, and deletion 20q were observed in 174 (24.4%), 173 (24.3%), 91 (12.8%), and 50 (7.0%) of the patients, respectively. Combined, 86.6% of the patients had one or more genetic lesions.

Patients with one or more mutations or CNVs showed unfavorable overall survival (Hazard Ratio (HR) 2.46, P = 2.12 x 10^-5). Univariate analysis for each gene identified mutations in TP53 (HR 2.85, P < 2.0 x 10^-16), NRAS (HR 1.90, P = 5.4 x 10^-4), ETV6 (HR 1.54, P = 0.029), CBL (HR 2.25, P = 5.3 x10^-5), EZH2 (HR 1.74, P = 0.014), KRAS (HR 2.01, P = 2.0 x 10^-3), U2AF2 (HR 1.97, P = 0.027), JARID2 (HR 2.09, P = 0.039), and RIT1 (HR 2.16, P = 0.023) as the unfavorable factors for the overall survival. Besides, mutations in PRPF8 had a favorable effect on overall survival (HR 0.50, P = 0.029). Then, we performed multivariate analysis with stepwise model selection of these significant mutations and clinical parameters. Mutations in TP53 (HR 2.31, P=0.015), and ETV6 (HR 2.57, P=0.015) remained significant together with complex karyotype (HR 2.15, P = 0.0063), grade of acute graft versus host disease (GVHD) (Grade I or II: HR 1.95, P = 0.011, Grade III or IV: HR 4.18, P = 7.94 x 10^-5), and the number of red blood cell transfusion received before HSCT (>=10 times:  HR 2.64, P = 0.027).

Next, we analyzed the impact of mutations on relapse in cases who achieved complete response after HSCT (N = 423 (58.8%)). Patients with mutations in one or more genetic lesions showed unfavorable relapse free survival (HR 2.27, P = 1.65 x 10^-4). Univariate analysis for each gene revealed mutations in TP53 (HR 3.09, P = 9.5 x 10^-16), NRAS (HR 2.21, P = 0.0019), ETV6 (HR 1.90, P = 0.012), PRPF8 (HR 0.40, P = 0.046), and WT1 (HR 2.24, P = 0.013) were significant for the relapse free survival. Multivariate analysis and stepwise model selection identified ETV6 (HR 2.98, P = 0.011), WT1(HR 4.01, P = 0.014), complex karyotype (HR 2.39, P = 0.0083), IPSS High (HR 6.22, P = 0.0053), and Grade III or IV acute GVHD (HR 2.91, P = 0.0071) as unfavorable factors.

Conclusions:

This large study of MDS cases treated by unrelated HSCT demonstrated that somatic mutations of several driver genes were novel prognostic factors for overall and relapse free survival. These genetic factors were independent of well-known prognostic makers, and therefore could be used to better guide therapy for MDS patients.