Patients with lower‐risk myelodysplastic syndromes (LR‐MDS) as defined by the International Prognostic Scoring System (IPSS) have more favorable prognosis in general, but significant inter‐individual heterogeneity exists. In this study, we examined the molecular profile of 15 MDS‐relevant genes in 159 patients with LR‐MDS using next‐generation sequencing. In univariate COX regression, shorter overall survival (OS) was associated with mutation status of ASXL1 (P = .001), RUNX1 (P = .031), EZH2 (P = .049), TP53 (P = .016), SRSF2 (P = .046), JAK2 (P = .040), and IDH2 (P = .035). We also found significantly shorter OS in patients with an adjusted TET2 variant allele frequency (VAF) ≥18% versus those with either an adjusted TET2 VAF <18% or without TET2 mutations (median: 20.4 vs 47.8 months; P = .020; HR = 2.183, 95%CI: 1.129‐4.224). After adjustment for IPSS, shorter OS was associated with mutation status of ASXL1 (P < .001; HR = 4.306, 95% CI: 2.144‐8.650), TP53 (P = .004; HR = 4.863, 95% CI: 1.662‐14.230) and JAK2 (P = .002; HR = 5.466, 95%CI: 1.848‐16.169), as well as adjusted TET2 VAF ≥18% (P = .008; HR = 2.492, 95% CI: 1.273‐4.876). Also, OS was increasingly shorter as the number of mutational factors increased (P < .001). A novel prognostic scoring system incorporating the presence/absence of the four independent mutational factors into the IPSS further stratified LR‐MDS patients into three prognostically different groups (P < .001). The newly developed scoring system redefined 10.1% (16/159) of patients as a higher‐risk group, who could not be predicted by the currently prognostic models. In conclusion, integration of the IPSS with mutation status/burden of certain MDS‐relevant genes may improve the prognostication of patients with LR‐MDS and could help identify those with worse‐than‐expected prognosis for more aggressive treatment.

Although cytarabine has been widely considered as one of the chemo drugs for high-risk myelodysplastic syndromes, the overall response rate is only 20%~30%. Nuclear factor erythroid 2-related factor 2 (NFE2L2, also called NRF2) has been shown to play a pivotal role in preventing cancer cells from being affected by chemotherapy. However, it is not yet known whether NFE2L2 has utility as a prognostic biomarker in myelodysplastic syndromes, or whether elevated NFE2L2 levels are associated with cytarabine resistance. Here, we found that NFE2L2 expression levels in bone marrow from high-risk patients exceeded that of low-risk myelodysplastic syndromes patients. Importantly, high NFE2L2 levels are correlated with inferior outcomes in myelodysplastic syndromes patients (n=137). Downregulation of NFE2L2 by the inhibitor Luteolin, or lentiviral shRNA knockdown, enhanced the chemotherapeutic efficacy of cytarabine, while myelodysplastic syndromes cells treated by NFE2L2 agonist Sulforaphane showed increased resistance to cytarabine. More importantly, pharmacological inhibition of NFE2L2 could sensitize primary high-risk myelodysplastic syndromes cells to cytarabine treatment. Mechanistically, downregulation of dual specificity protein phosphatase 1, a NFE2L2 direct target gene, could abrogate cytarabine resistance in NFE2L2 elevated myelodysplastic syndromes cells. Silencing NFE2L2 or dual specificity protein phosphatase 1 also significantly sensitized cytarabine treatment and inhibited tumors in myelodysplastic syndromes cells transplanted mouse models in vivo. In conclusion, our study suggests that targeting NFE2L2 in combination with conventional chemotherapy could pave the way for future high-risk myelodysplastic syndromes therapy.