PTPN12 Is Targetable and Context-Specific TSG in -7/del7q Myeloid Neoplasia

The complete or partial loss of chromosome 7 is a common and devastating genetic lesion in myeloid neoplasias (MN) that confers substantially poorer prognoses. These lesions can be identified as either a founding or secondary loss in 5-12% of myeloid neoplasia subtypes such as primary and secondary acute myeloid leukemia, myeloid dysplastic syndrome, and myeloproliferative neoplasia, as well as 83% of MN with an aplastic anemia background (Mori et al., 2023). Despite many efforts to elucidate the pathogenesis of -7/del7q lesions, our understanding remains incomplete and no targeted therapies are available to these patients.

To identify missing components of the -7/del7q pathogenesis puzzle, we combined an in-house patient databank with external sources of myeloid neoplasia whole exome sequencing to create a cohort of 47 -7/del7q patients. Within this dataset, we queried all chromosome 7 genes for pre-existing loss-of-function (LOF) mutations and then determined if the mutant or wild-type allele was preferentially lost. A significant preference for loss of the wild-type allele suggests the gene is acting as a tumor suppressor, wherein biallelic inactivation provides an oncogenic advantage. Among the hits for this analysis was protein tyrosine phosphatase non-receptor type 12 (PTPN12), a widely studied TSG in many contexts, but with high expression and no apparent association with survival or upregulation in pan-AML analyses (Arora et al., 2012; Liu et al., 2023). PTPN12 LOF is prognostic of poor outcomes in several cancers including non-small cell lung cancer, bladder transitional cell carcinoma, and prostate cancer and has been mechanistically characterized in several more such as osteosarcoma, glioblastoma, and nasopharangeal carcinoma (Sun et al., 2011; Su et al., 2013; Chen et al., 2018; Lin et al., 2018; Liu et al., 2023). Most notably, PTPN12 mutation is very common in triple negative breast cancer and systematic inhibition of its targets, mimicking its physiological function, resulted in tumor regressions in chemo-refractory patient-derived TNBC models (Sun et al., 2011; Wu et al., 2013; Nair et al., 2018).

To confirm its tumor suppressor properties and dissect the biological functions we knocked out PTPN12 in a -7/del7q cell model, KG1, with high (76.6%) and low (4.7%) efficiency. We used the high efficiency knockout to assay cell proliferation effects of LOF of PTPN12 in a -7/del7q context and demonstrated an 18.0% increase in proliferation rate. This proliferative advantage is substantial given the highly evolved cell model of malignancy. The low efficiency knockout population was cultured for 21 days and re-checked for variant allele frequency. The PTN12^-/- fraction increased from 4.7% to 22.6%, again demonstrating the strong proliferative advantage of PTP12 LOF.

As a cytosolic phosphatase capable of inhibiting multiple cell-signaling pathways, PTPN12 activation may cause substantial inhibition of cell proliferation. To directly assay the effects of PTPN12’s phosphatase activity of cell-signaling, we utilized the phosphatase activator DT-061 in models of del7q MN (KG1, featuring low PTPN12 expression), -7 MN (F36P, featuring moderate PTPN12 expression), and chromosome 7 diploid MN (THP1, featuring high PTPN12 expression). At 10uM, a 72-hour viability and proliferation analysis revealed a stark inverse relationship between PTPN12 expression and cell proliferation/viability.

Together, these results indicate that PTPN12 may be a critical TSG contributing to -7/del7q leukemogenesis. As an overlooked contributor to -7del7q leukemogenesis, PTPN12 may represent a small-molecule targetable therapeutic option for a patient population in dire need.