Comparison of the Molecular Spectrum of Lenalidomide-Treated Myelodysplastic Syndrome with and without Del(5q)

Background: Lenalidomide (LEN) is an immunomodulatory drug which binds cereblon through a glutarimide ring modulating the substrate specificity of CRL4^CRBNE3 ubiquitin ligase complex, resulting in the proteosomal degradation of specific disease-related proteins. LEN is approved for the treatment of RBC transfusion-dependent (TD) low and int-1 risk MDS patients with del(5q), 70% of whom reach RBC transfusion-independence (TI) and 50% complete cytogenetic remission. It is also under investigation in RBC -TD low and int-1 risk MDS without del(5q) resistant to erythropoietin stimulating agents and with 20-30% of patients reaching RBC-TI. Herein we aimed to study whether molecular mutations in MDS patients with and without del(5q) influenced the response to LEN treatment.

Methods: We collected 95 MDS patients treated with LEN, 72 with del(5q) and 23 without del(5q) (23/23: normal karyotype, presence of ringed sideroblasts and SF3B1^MUT). Retrospective clinical information was available for 65 patients. To characterize the mutational spectrum of patients with del(5q) and non del(5q), we combined results from multi amplicon targeted sequencing Ion Torrent (44 cases) and from captured-based targeted deep sequencing (51 cases). The Ion Torrent panel included 39 of the most frequently mutated genes in MDS (ASXL1, BCOR, BRAF, CBL, CDKN2A, CEBPA, DNMT3A, ETV6, EZH2, FLT3, GNAS, IDH1, IDH2, JAK2, KIT, KRAS, LUC7L2, MPL, NF1, NPM1, NRAS, PHF6, PTPN11, RAD21, RPS14, RUNX1, SETBP1, SF1, SF3A1, SF3B1, SMC3, SPARC, SRSF2, STAG2, TET2, TP53, U2AF1, WT1, ZRSR2). The Ion Torrent panel was then extended for the captured-base sequencing and updated with the addition of 43 genes including BCORL1, CALR, CSNK1A1 and KDM6A. The average depth per gene was 780x per sample.

Results: Patients with del(5q) vs. non del(5q) had an equal risk distribution (LR: 46/55 vs. 21/22; HR: 9/55 vs. 1/22). We restricted our analyses to LR patients. Median age was 69 yrs (34-90) and M:F ratio was 15:50. A significantly higher median of hemoglobin (Hb) levels were found in del(5q) in comparison to non del(5q) patients (9 g/dL (6-13) vs. 8 g/dL (7-9); P=.001). Molecularly we found that a slightly lower number of mutations occurred in del(5q) [2 mutations (0-6)] compared to the number of mutations in non del(5q) [3 mutations (1-7); P=.001]. WHO 2008 distribution was significantly (P<.001) different between del(5q) and non del(5q) patients, being del(5q) overrepresented by the MDS with isolated del(5q) (74%, 34/46) group while non del(5q) was overrepresented in RARS (67%, 14/21) group.

We then compared responders vs. non-responders. LEN median treatment was 10 mo. (3-48 mo.), with an overall follow-up of 4 years (4mo.-10 yrs). As expected, LEN response rate was significantly (P<.001) higher in patients with del(5q) (86%; 25/39) than with non del(5q) (14%; 4/23) patients. Responders showed a significant improvement in Hb levels in comparison to non-responders (N=27 vs. N=32; 9 g/dL (6-12) vs. 8 g/dL (5-10); P=.05), and a lower median number of mutations [3 mutations (1-5)] rather than responders [2 mutations (0-7)]. According to the WHO 2008, responders were significantly (P=.001) grouped in MDS with isolated del(5q) while non-responders were in between RARS (13/29) and RCMD (11/29).

We then selected mutated genes present in at least 3 patients. CSNK1A1 (2), BCOR (3), CTCF (3) CUX1 (3), JAK2 (9) KIT (3) and TP53 (11) were restricted to the del(5q) patients. No genes were restricted to non del(5q) group. However, those genes in both groups [del(5q) vs. non del(5q)] were significantly more mutated in non del(5q) group rather than in del(5q) group: ASXL1 (N=6/23 vs. N=4/72; P=.005) and TET2 (N=9/23 vs. N=8/72; P=.002). CSNK1A1 (2) and MECOM (2) genes were restricted to the responders group. CTCF (3), SRSF2 (3), GNAS (2) and IDH2 (2) were only represented in the non-responders group. Genes significantly mutated in non-responders vs. responders were TET2 (N=11/33 vs. N=2/29; P=.011) and TP53 (N=6/33 vs. N=1/29; P=.069).

Conclusion: In conclusion, this multicenter study describes that del(5q) and non del(5q) have a different mutational profile although no unifying somatic defect was found. Moreover, non-responders patients had a higher number of mutations and a higher percentage of TET2 and TP53 mutations while responders showed some unique mutations.