PPM1D Mutations and up Modulation Phenocopy TP53 Lesions in Myeloid Neoplasms

Similar to many non-hematologic malignancies, TP53 mutations also arise in myeloid neoplasms (MN). Loss of function or hypomorphic TP53 mutations confers risks of both malignancy onset and accelerated progression to more aggressive disease. To exert full oncogenic function, somatic or inherited (Li-Fraumeni syndrome) heterozygous TP53 mutations require inactivating second allele hits, e.g ., uniparental disomy (UPD) or deletions. Recently, mutations in PPM1D, which encodes P53-induced protein phosphatase-1 (WIP-1), were reported in non-hematologic neoplasms and healthy controls with clonal hematopoiesis. The mutations are mostly inactivating hits due to truncation via nonsense or frame shift mutations. PPM1D is located in 17q23.2 and encodes for a PP2c family serine/threonine phosphatase that has a direct inhibitory effect on key members of the check point pathway, including TP53, CHK1 and CHK2. As most of the mutations are in the C-terminal domain, upon truncation, the N-terminal catalytic phosphatase domain remains and is overexpressed due to a compensatory mechanism. The increased phosphatase activity prevents TP53 activation by kinases and thus, overall, inhibits its function. Truncating PPM1D mutations are thus expected to have effects similar to those of TP53 losses of function.

Our study goal was to elucidate how PPM1D mutations along with TP53 lesionsshape the phenotype of patients with MNs. In 2,709 MNs, 6% (163/2,709) of cases harbored TP53 and 1.6% (43/2,709) PPM1D mutations. UPD and deletions of TP53 locus were present in 12%, while biallelic hits in 10% of mutant cases. All PPM1D mutations were heterozygous. TP53 and PPM1D mutations were mutually exclusive, but were common in tMDS/AML (therapy related myelodysplastic syndrome/acute myeloid leukemia) found in 13.5% and 4.4% of patients, respectively; Of note is that TP53 mutations were mostly enriched in patients with history of chemotherapy rather than radiation (see our abstract on tMN: Kuzmanovich et al). No PPM1D mutations were found in MDS or AML, where TP53 was present in 6% of patients.

Using publicly available GEO datasets GSE19429 (183 MDS cases) and GSE13159 (253 MDS and 351 AML cases), we sought correlations between high PPM1D mRNA and PPM1D truncations. Using the mean + standard deviation as the cut-off for calling an mRNA level overexpressed, overexpression was found in 24% of MDS and 21% of AML. In a subset analysis of AML, the frequency of PPM1D mutations was significantly higher in AML with complex vs. normal karyotypes (38% vs. 17%; Odds ratio 3.5 (95%CI: 1.7-7.0; P=.0005).

TP53 and PPM1D mutations are functionally related but mutually exclusive and arise across a similar spectrum of MNs, specifically tMN. PPM1D mutations and high PPM1Dexpression are involved in MN pathogenesis. TP53 hits can be ancestral or secondary in spontaneous MDS/AML. PPM1D mutations are somatic, exclusively present in tMN, and thus TP53 and PPM1D mutations are enriched in tMDS, likely because chemotherapy exerts systemic selective pressure for apoptosis resistant cells. It is possible that preexisting tiny clones with biallelic T P53 mutations are being selected for chemotherapy. Current technologies are not able to distinguish small homozygous clones from large heterozygous clones.