Uncovering TP53 Mutations in MDS, AML Requires NGS

TP53-targeted treatment options represent an unmet need for patients with myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). However, identifying the mutation, which presents in 8% to 12% and 5% to 10% of MDS and AML cases, respectively,¹ by next-generation sequencing (NGS) remains an important component of shaping a patient’s treatment course, according to David Sallman, MD.

“People could argue that there is no therapy specifically approved for TP53-mutant disease. If they are going to give any patient with highrisk MDS a hypomethylating agent [HMA] such as azacitidine, then they don’t think that sequencing necessarily matters, but it does have prognostic implications,” said Sallman, an assistant member in the Department of Malignant Hematology at Moffitt Cancer Center in Tampa, Florida, in an interview with OncLive.

“Median overall survival for patients with high-risk, TP53-mutant MDS and AML is less than 1 year. That’s significantly worse than all other subtypes,” Sallman added.

HMA therapy is the standard of care for patients with high-risk MDS; however, TP53-mutant disease treated with HMAs infrequently achieves durable clonal suppression and typically has poor overall survival (OS).² The efficacy of standard treatment is commensurately lacking in AML. Moreover, TP53 mutations are known to not only confer resistance to cytotoxic chemotherapy but also correlate with poor responses to induction chemotherapy in MDS and AML. The complete response rate for TP53-mutant, induction chemotherapy– treated AML spans 20% to 40% with high relapse rates; median OS ranges from 4 to 9 months.¹

Beyond HMAs and chemotherapy, TP53 alterations also complicate the pursuit of allogeneic hematopoietic stem cell transplantation (allo-HSCT).^1,2 Across de novo MDS and therapy-related MDS, TP53 is the only somatic gene mutation to predict not only inferior OS but also suboptimal benefit from allo-HSCT.³ Poor long-term outcomes seen with allo-HSCT in TP53-affected AML have discouraged the execution of the process in this patient subgroup, with 2 studies demonstrating early relapse, with post-transplant relapse rates of 50% and 40% at 100 days and 6 months after allo-HSCT, respectively.¹

“The presence of a TP53 mutation has significant impact in the consideration of a clinical trial,” Sallman said. “Patients who have a TP53 mutation and are getting standard treatment are likely not going to do very well, and so they really need to see if there is any alternative option that can be considered. We strongly recommend clinical trials given the poor outcomes to standard therapy.”

Although Sallman maintains that it is “really important to get the sequencing result before making treatment decisions,” he acknowledges that the amount of time required to receive NGS results can be an obstacle to therapeutic expeditiousness. “Whereas an NGS platform at an academic center typically can turn around results between approximately 4 and 10 days, commercial labs can sometimes take 2 to 3 weeks. So, I think trying to identify these patients quickly can be a challenge. Some of these patients have severe cytopenias and do require quite urgent therapy,” Sallman explained.

Testing for TP53 Mutations

The National Comprehensive Cancer Network (NCCN) “highly recommends” genetic testing for somatic mutations in genes associated with MDS⁴ and in AML. The NCCN also advises that all patients with AML should be tested not only for TP53 alterations, but also for c-KIT, FLT3-ITD, FLT3-TKD, NPM1, CEBPA, IDH1/2, RUNX1, and ASXL1 on the basis that these mutations are “associated with specific prognoses in a subset of patients and may guide treatment decisions.”⁵

In the MDS guidelines, the NCCN also recommends additional molecular and genetic testing for hereditary hematologic malignancy predisposition in younger patients to determine whether a germline predisposition disorder for myeloid neoplasms and solid tumor cancers is at play. This includes, Li-Fraumeni syndrome, for example, which is associated with TP53-mutant MDS and AML.⁴

NGS is the standard modality for identifying TP53 mutations, according to Sallman: “Every panel, both commercial and academic, will include analysis of TP53; it was 1 of the first 5 genes to be evaluated so it’s really a standard, but you have to have an NGS panel because there are thousands of different potential mutations for TP53. Basically, all labs have a cutoff of 5%. It’s pretty standard that 5% or higher signals a positive mutation,” Sallman said.

By contrast with other targets such as IDH1/2 that have hotspots, thereby enabling the use of a polymerase chain reaction assay, TP53 “requires an NGS platform for detection,” Sallman said. Although immunohistochemistry is “a good surrogate” to identify patients who are likely to have a TP53 mutation, “the only true way to know yes or no is to do the sequencing via NGS,” he added.

NGS Adoption

“In the NCCN guidelines, it is standard to perform NGS sequencing for patients with MDS and AML at least at baseline, and to then think about the disease sequentially,” Sallman said. “All patients should have this analysis done at baseline and potentially again if there is disease progression.”

NGS uptake nevertheless varies by clinical setting, despite NCCN backing. At academic centers, NGS is customary for patients with MDS and AML and is performed for nearly all patients, according to Sallman. Conversely, NGS is not as widely used in community oncology clinics. “It’s still not uniform. There are still some community centers that don’t necessarily assess TP53 as a standard test,” Sallman said. However, NGS use in these instances is “continuing to increase in frequency,” he observed.

The inconsistent application of NGS is a current challenge in the TP53-mutant MDS and AML landscapes, but Sallman is optimistic that ongoing efforts to develop targeted therapies for this population will galvanize greater uptake of the modality. “I think, as more drugs with a molecular focus get approved, NGS is going to become a standard. We saw it happen when FLT3 and IDH1 [biomarkers] and 2 inhibitors were approved in AML. Then testing for all of those aberrations became standard in what felt like overnight. So, I think it’s really the treatment option that informs the identification of mutations,” Sallman said.

In settings where NGS for MDS and AML is not frequently performed, health care providers should be aware of the clinical indicators that could suggest TP53-mutant disease and subsequently guide a patient to sequencing. “We have observed in patients with excess blast MDS with high ringed sideroblasts a strong correlation with TP53 mutations,” Sallman explained. Cytogenetic abnormalities can also signal TP53-mutant disease. Aberrances in chromosomes 5, 7, and 17 are also “highly concordant with the presence of a TP53 mutation and can be observed [via a fluorescence in situ hybridization panel], which can be turned around in about 1 to 2 days,” he added.

High numbers of blasts or ringed sideroblasts or cytogenetic abnormalities are not surrogate markers for diagnoses of TP53-mutant disease based on NGS results. These findings are clinical cues that the patient could belong to this molecularly specific subset of the MDS and AML population. Given the prognostic and therapeutic implications of a TP53 mutation, providers should not only be aware of the predictors of TP53 alterations, but also actively look for them when patients present with MDS or AML, Sallman concluded.

References

1. Hunter AM, Sallman DA. Current status and new treatment approaches in TP53 mutated AML. Best Pract Res Clin Haematol. 2019;32(2):134-144. doi:10.1016/j. beha.2019.05.004
2. Hunter AM, Sallman DA. Targeting TP53 mutations in myelodysplastic syndromes. Hematol Oncol Clin North Am. 2020;34(2):421-440. doi:10.1016/j.hoc.2019.11.004
3. Sallman DA, Al Malki M, Asch A, et al. Tolerability and efficacy of the first-in-class anti-CD47 antibody magrolimab combined with azacitidine in MDS and AML patients: phase 1b results. J Clin Oncol. 2020;38(suppl 15):7507. doi:10.1200/JCO.2020.38.15_suppl.7507
4. NCCN. Clinical Practice Guidelines in Oncology. Myelodysplastic syndromes, version 1.2021. Accessed October 8, 2020. https://www.nccn.org/professionals/ physician_gls/PDF/mds.pdf 
5. NCCN. Clinical Practice Guidelines in Oncology. Acute myeloid leukemia, version 4.2020. Accessed October 8, 2020. https://www.nccn.org/professionals/physician_gls/ pdf/aml.pdf