Genetic Screening for Synthetic Lethal Partners of Polynucleotide Kinase/Phosphatase: Potential for Targeting SHP-1–Depleted Cancers

Abstract

A genetic screen using a library of 6,961 siRNAs led to the identification of SHP-1 (PTPN6), a tumor suppressor frequently mutated in malignant lymphomas, leukemias, and prostate cancer, as a potential synthetic lethal partner of the DNA repair protein polynucleotide kinase/phosphatase (PNKP). After confirming the partnership with SHP-1, we observed that codepletion of PNKP and SHP-1 induced apoptosis. A T-cell lymphoma cell line that is SHP-1 deficient (Karpas 299) was shown to be sensitive to a chemical inhibitor of PNKP, but resistance was restored by expression of wild-type SHP-1 in these cells. We determined that while SHP-1 depletion does not significantly impact DNA strand-break repair, it does amplify the level of reactive oxygen species (ROS) and elevate endogenous DNA damage. The ROS scavenger WR1065 afforded protection to SHP-1-depleted cells treated with the PNKP inhibitor. We propose that codisruption of SHP-1 and PNKP leads to an increase in DNA damage that escapes repair, resulting in the accumulation of cytotoxic double-strand breaks and induction of apoptosis. This supports an alternative paradigm for synthetic lethal partnerships that could be exploited therapeutically. Cancer Res; 72(22); 5934-44. Ó2012 AACR.

Evolutionary and Structural Analyses of Mammalian Haloacid Dehalogenase-type Phosphatases AUM and Chronophin Provide Insight into the Basis of Their Different Substrate Specificities

“…Despite their important roles in human diseases, which make some HAD phosphatases conceptually attractive drug targets (5,12,25,70,71), knowledge of mammalian HAD phosphatase specificity determinants is currently very limited. We demonstrate that HAD substrate specificity can be encoded by a very small number of predictable amino acid residues.…”

Base excision repair and its implications to cancer therapy

“…One such inhibitor, A12B4C3, with an IC 50 of ∼10 µM acts as a radiosensitizer in response to densely ionising carbon ion irradiation in prostate cancer cells [ 51 ], and Auger-emitting radioimmunotherapy in human myeloid leukaemia cells [ 52 ]. Synthetic lethal partnerships of PNKP with PTEN in colon cancer cell lines, and with the protein tyrosine phosphatase SHP-1 in T-cell lymphoma cell line have been identified, and where the combination of deficiencies in these proteins with A12B4C3 is effective in cell killing [ 53 , 54 ]. Interestingly, methods of delivering inhibitors of PNKP directly to the tumour through micelle encapsulation of the drug have been described, which are capable of radiosensitizing colon cancer cells [ 55 ].…”

Mining the function of protein tyrosine phosphatases in health and disease

“…These included DUSP-5, INPP5A, MTMR7, PPP6C, and PSPH. The SH2 domain-containing tyrosine phosphatase-1 (SHP-1) was also identified as a potential synthetic lethal partner of the DNA repair protein polynucleotide kinase/phosphatase using a “druggable” genome siRNA library that comprises of 205 phosphatases, 696 kinases, 490 G-protein-coupled receptors and 5,570 uncategorized proteins [35]. …”