IDH1 and IDH2 : Founding or Progressor Mutations in Myeloid Neoplasms

IDH1/2 genes normally regulate cellular metabolism and epigenetic expression. Mutations in IDH1/2 are believed to play a significant part in leukemogenesis, and inhibitors are in active development. IDH1/2 mutations are rarely the sole mutation in myeloid neoplasms and are frequently found with co-mutations in other genes. However, it is not clear if the IDH1/2 mutations are founder or progressor mutations. Determining whether an IDH1/2 mutation is a founder or progressor may have significant impact on therapy outcome. As founding mutations persist in subclones, targeting founding mutations is likely to result in the eradication of the leukemic clone, whereas targeting progressor mutations can only destroy the subclone and progeny. We used variant allele frequency (VAF) and next generation sequencing (NGS) to determine if IDH1/2 mutations are founding or progressor mutations and to characterize the co-mutational background for 6390 patients who presented with a clinical impression of myeloid neoplasm.

Methods: A total of 6390 consecutive bone marrow aspirate samples or peripheral blood samples submitted with clinical impression of AML, MDS, or MPN between January 2014 and mid 2017 were tested for mutations in myeloid genes using NGS. We used the TruSight Myeloid Panel (Illumina, San Diego, CA) for detecting missense mutations and fragment length analysis (FLA) for detecting ITD in FLT3 and large indels in CALR . DNA was extracted from samples using the QIAamp DNA Mini Kit. This NGS testing covers mutations in 54 myeloid-related genes. The average depth of sequencing was 10,000x.

Results: A total of 2670 (42%) of the tested samples showed a mutation in one or more of the tested genes. Of the samples with mutations 467 patients (17.5%) patients showed mutations in either IDH1 or IDH2 genes. IDH1 mutations were detected 185 (40%) and IDH2 was detected in 291 (62%) of these patients. Nine patients (2%) had mutations in both IDH1 and IDH2. To distinguish patients with IDH1/2 as a founder mutation vs. subsequent (progressor) mutation, we used a lower VAF of a 10% in IDH1 or IDH2 as compared with the average VAF of all genes as a cut-off. Using this criteria, we found patients 35 patients (19%) as a progressor in the IDH1 mutated group and 48 (16.5%) in the IDH2 mutated group as progressors. Only 12 patients (6.5%) of the IDH1 mutated patients and 11 (4%) of the IDH2 mutated patients had IDH1 or IDH2 as the sole mutated gene.

The most commonly co-mutated genes with IDH1/2 were DNMT3A, SRSF2, NPM1, ASXL1, and RUNX1 detected in 34%, 28%, 22%, 22%, and 20%, respectively. Mutations in TP53 and FLT3, which may have significant impact on therapy and outcome, were detected in 7% and 12% of patients, respectively. In patients with an IDH1/2 progressor mutation, there was significantly higher relative mutations in TP53 (P=0.03) and FLT-ITD (P=0.0001). The presence of mutations in TP53 and FLT-3 -ITD signify significantly more aggressive myeloid neoplasm or acute leukemia. In addition to the typical mutations in codon 132 of IDH1 and codons 140 and 132 in IDH2, we detected mutations by NGS in codons 100, 103, 109, and 183 in IDH1 and codon 173 in IDH2 .

Conclusion: IDH1/2 mutations are founding mutations in most myeloid neoplasms. However, 19% of patients with IDH1/2 mutations may have acquired their IDH1/2 mutations in a subclone. Majority of these patients have mutations in FLT-3-ITD and TP53 and may represent significantly more aggressive disease. Clinical studies are needed to determine the pattern of response to IDH1/2 inhibitors in patients with subclonal (progressor) mutation in IDH1/2 . The potential of selecting for the leukemic clone that lack IDH1/2 mutation should be considered. Complete molecular profiling rather than testing for mutations in IDH1/2 alone provides important information in the management and therapy of myeloid neoplasms.

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