The advent of high-throughput gene sequencing has revolutionized our understanding of the genetic mutations that drive myeloid malignancies. While these mutations are of interest pathobiologically, they are increasingly being recognized as clinically meaningful in providing diagnostic, prognostic, and therapeutic information to guide patient care. In this first part of our two-part review, we introduce mutation profiling as a relevant clinical tool for hematologists treating patients with myeloid malignancies. Next, we discuss the diagnostic and prognostic role of mutation profiling in myelodysplastic syndrome and acute myeloid leukemia. Finally, we detail the therapeutic implications of specific mutations in myelodysplastic syndrome and acute myeloid leukemia. In Part 2, we will discuss similar clinical approaches using mutation profiling in myeloproliferative neoplasms and other myeloid malignancies.
Enormous strides have been made in recent years that have furthered our understanding of the underlying genetic alterations driving myeloid malignancies. High-throughput gene sequencing, the technological innovation behind these advances, has resulted in the identification of numerous recurrent somatic pathogenetic mutations. Genes that are frequently mutated in myeloid malignancies possess a multitude of cellular functions that can be generally grouped into those that regulate 1) RNA, 2) the transcriptome, and 3) the epigenome (Figure 1). With a growing appreciation of the biological consequences of these mutations, there is also heightened recognition of their clinical implications in the management of patients with myeloid malignancies such as myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), myeloproliferative neoplasms, and other related myeloid neoplasms. Molecular abnormalities identified in the blood and bone marrow cells of patients with myeloid malignancies can provide diagnostic and prognostic clues[2,3] and therapeutic direction to the clinician. Therefore, understanding the clinical relevance of molecular testing holds the potential to greatly personalize the care of these patients. Despite the routine incorporation of mutation profiling in the clinic, questions remain regarding its optimal use in the care of an individual patient with a myeloid malignancy. By describing the current landscape of relevant genomic alterations in myeloid malignancies, we hope to provide guidance and clarity to clinicians struggling to understand the clinical ramifications of mutation profiling for their patients.
MDS: Prognostic Implications
The International Prognostic Scoring System (IPSS) has been used as a prognostic tool to guide therapeutic decision making based on inherent risk associated with MDS. It incorporates conventional cytogenetics, bone marrow blast percentage, and peripheral blood count parameters. More recently, the IPSS has been revised (and validated) to include updated cytogenetic information and more detail on depth of cytopenias and degree of blast percentage (Table 1). None of the current risk stratification tools incorporates genomic data.[7,8] However, our understanding of the molecular pathogenesis of MDS has grown over the past decade with the identification of recurrent mutation events. The most common mutated genes in MDS include those involved in DNA methylation (TET2, DNMT3A, and IDH1/2), chromatin modification (ASXL1, EZH2), transcriptional regulation (RUNX1, TP53), signal transduction (NRAS, KRAS), and RNA splicing (SF3B1, SRSF2) (Table 2).
Information regarding mutations can also have prognostic significance in MDS (Table 3). For example, mutations involving TET2 have been shown to be associated with a favorable prognosis in some studies, although they were neutral in others. MDS patients harboring TET2 mutations had a longer overall survival (OS) than patients without such mutations, independent of age, IPSS score, and transfusion requirements. Additionally, the absence of TET2 mutations was associated with a fourfold increased risk of death. In contrast, a more recent and larger study did not identify a significant OS difference in MDS patients with monoallelic or biallelic TET2 mutations vs those without such mutations.
DNMT3A is an epigenetic modulator that encodes for DNA methyltransferase 3 alpha. An investigation of 150 de novo MDS cases demonstrated that those patients with DNMT3A mutations had worse OS and more rapid evolution to AML. However, this prognostic value may vary based on the presence of concurrent mutations and the IPSS risk group. For example, mutated SF3B1 co-occurring with mutated DNMT3A may mitigate the negative effect of DNMT3A mutations on survival in a lower-risk population (4.16 years vs 1.45 years; P = .35).
Similar to TET2 and DNMT3A, IDH1/2 mutations lead to global DNA hypermethylation. Mutations involving IDH1/2 are associated with a shorter OS and a higher rate of transformation to AML. Recent analysis of data from 3,000 MDS patients found that IDH2 mutations were associated with shorter OS. In contrast, the association between IDH1 mutations and shorter OS did not reach statistical significance, highlighting the variation in impact of mutations occurring in similar genes. Additionally, a study of patients with MDS or secondary AML who received hematopoietic stem cell transplantation (HSCT) suggested that the presence of mutated IDH2 after HSCT may be associated with reduced OS (hazard ratio, 2.6). This negative prognostic impact has not been observed for mutated IDH1.
ASXL1 and EZH2 are epigenetic modulators that act through histone modification and are significant predictors of poor OS after adjustment for IPSS risk group. RUNX1 has also been studied in MDS patients. Those with mutated RUNX1 had higher neutrophil counts and higher frequency of -7/7q deletion than those with wild-type RUNX1, and the presence of the mutant allele was closely associated with a shorter OS.[16,17]
TP53 mutation has been shown to be more predictive of OS than IPSS score. Patients with MDS harboring a TP53 mutation had shorter leukemia-free survival than those with wild-type status. Moreover, patients with normal karyotype and TP53 mutations survived for a similarly short period (median, 9.8 months) compared with patients who had a complex karyotype and TP53 mutations (median, 7.6 months). In a retrospective study of the outcome after HSCT in 87 MDS patients, the presence of TP53, TET2, and DNMT3A before transplant were all independently associated with reduced OS after transplant. SF3B1 and SRSF2 encode components of the nuclear ribonucleoprotein integral to the spliceosome. SF3B1 mutations are present in over 20% of MDS patients and more specifically in 81% of those with refractory anemia with ring sideroblasts (RARS) or refractory cytopenia with multilineage dysplasia and ring sideroblasts.[9,22] Patients with SF3B1 mutations have a significantly better OS and a reduced incidence of disease progression than patients lacking them. SRSF2 mutations, detected in 12% to 15% of MDS patients, are associated with an inferior OS, especially in the lower-risk IPSS group; this may be attributed to the close association of SRSF2 mutations with advanced age.[23,24]
AML: Prognostic Implications
Cytogenetic-based risk stratification remains the mainstay of risk-adapted treatment strategies in AML (Table 4). Numerous studies have examined the clinical impact of mutated NPM1, FLT3, and IDH1/2 in AML. The presence of mutated NPM1 is associated with a higher rate of complete remission after induction chemotherapy. When mutated NPM1 coexists with wild-type FLT3, it is an independent predictor of favorable OS and event-free survival. Additionally, when NPM1 is mutated along with IDH1/2, it is associated with improved 3-year survival in intermediate-risk (by karyotype) AML compared with mutated NPM1 with wild-type IDH1/2.
The presence of NPM1 transcripts can also signal submicroscopic minimal residual disease. This was demonstrated in a recent study of 346 patients with NPM1-mutated AML in which reverse-transcriptase quantitative polymerase chain reaction was used to detect residual NPM1 transcripts. Minimal residual disease at first complete response (CR) was detected in 16% of patients and associated with a higher risk for relapse at 3 years (82% vs 30%) and lower rate of survival (24% vs 75%). It was also an independent predictor of death in a multivariate analysis.
FLT3 mutation status is an important molecular variable to consider in AML patients classified as intermediate risk by cytogenetic-based risk stratification. Overall, the FLT3 internal tandem duplication (FLT3-ITD) mutation is associated with an unfavorable prognosis and is useful to further segregate higher-risk patients who may benefit from more aggressive therapy. FLT3-ITD has also been shown to be predictive of poor response to induction chemotherapy and HSCT.
A meta-analysis of 8,121 patients demonstrated that patients with mutations in IDH1 have an inferior OS when compared with patients who do not have this mutation. Mutated IDH2, interestingly, is associated with improved survival and decreased rate of relapse; however, when it occurs in conjunction with FLT3-ITD, this survival benefit is negated.
DNMT3A is a commonly mutated gene in AML, clustering within the intermediate-risk cytogenetic category, and overall is associated with inferior survival. However, this relationship is also affected by coexisting mutations. In high-risk patients with FLT3-ITD and NPM1 mutations, DNMT3A mutations are associated with decreased OS, relapse-free survival, and CR.
Mutated TET2 occurs in approximately 13% of AML patients with intermediate-risk cytogenetics and is associated with a poor prognosis in them, especially when coexisting with FLT3-ITD, NPM1 wild-type, or other unfavorable genotypes. A recent analysis of patients with normal-karyotype AML undergoing induction chemotherapy demonstrated that a homozygous TET2 mutation (approximately 25% of mutated TET2 cases) is an independent predictor of relapse.
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