Gene Expression and Mutation Analysis (GEMA) –Guided Precision Medicine Targeting PARP1 to Induce Synthetic Lethality in DNA-PK –Deficient Quiescent and BRCA-Deficient Proliferating Leukemia Stem and Progenitor Cells

Leukemia stem cells (LSCs), and especially quiescent LSCs, have a dual role as tumor initiating and therapy-refractory cells. Therefore, even if anti-tumor treatment clears a disease burden consisting mostly of proliferating leukemia progenitor cells (LPCs), it usually fails to eradicate therapy-refractory LSCs and also therapy-resistant LPCs.

LSCs, including quiescent LSCs and LPCs accumulate high numbers of spontaneous and drug-induced DNA lesions, including highly lethal DNA double-strand breaks (DSBs). Thus, LSCs and/or LPCs may be “addicted” to particular DNA repair mechanisms and targeting these pathways could sensitize LSCs to the lethal effect of unrepaired DSBs.

DSBs are usually repaired by two major mechanisms, homologous recombination repair (HRR) and non-homologous end-joining (NHEJ). While NHEJ plays a major role in quiescent cells, HRR works predominantly on broken replication forks in proliferating cells. Normal quiescent cells employ DNA-PK (PRKDC, XRCC5, XRCC6, LIG4) –mediated NHEJ to repair DSBs whereas PARP1-dependent NHEJ serves as back-up. Normal proliferating cells use PARP1-mediated base excision repair (BER) to prevent DSBs at collapsed replication forks, whereas BRCA (BRCA1, BRCA2, PALB2, RAD51 paralogs, RAD51)-mediated HRR serves as back-up to repair stalled/broken forks. The existence of these pathways creates the opportunity to apply “synthetic lethality” triggered by PARP1 inhibitors (PARP1i) in DNA-PK –deficient therapy-refractory quiescent LSCs and BRCA-deficient therapy-resistant proliferating LSCs/LPCs. This hypothesis is supported by PARP1i-mediated synthetic lethality in BRCA1-/- proliferating and XRCC6-/-quiescent cells.

Since inactivating mutations in BRCA and DNA-PK pathways are rather rare in leukemias we hypothesize that Gene Expression and Mutation Analysis (GEMA) can identify individual patients with leukemias displaying “spontaneous” and oncogene-induced downregulation of DSB repair genes which will be sensitive to “synthetic lethality” triggered by PARP1i +/- already approved drugs.

GENE EXPRESSION ANALYSIS: Global mRNA microarrays and qRT-PCR followed by immunofluorescent protein staining identified primary AMLs and ALLs from individual patients displaying BRCA- and/or DNA-PK –deficient phenotype (downregulation of at least one member of BRCA and/or DNA-PK pathway). Quiescent DNA-PK –deficient LSCs and proliferating BRCA-deficient LSCs/LPCs, but not DNA-PK and BRCA –proficient counterparts were sensitive to olaparib and BMN673 +/- already approved drugs.

GENE MUTATION ANALYSIS: BCR-ABL1 downregulates BRCA1 and DNA-PKcs proteins, FLT3(ITD) inhibits BRCA1 protein, and MLL-AF9 and AML1-ETO reduce BRCA2 and XRCC6 proteins, whereas HOXA9+MEIS1 do not affect the expression of DSB repair proteins. These effects were associated with reduced colony formation by BCR-ABL1, MLL-AF9 and AML1-ETO –transformed, but not HOXA9+MEIS1-treasformed Parp1-/-murine bone marrow cells. PARP1i olaparib and BMN673 +/- approved drugs induced DSBs resulting in abrogation of cell proliferation and/or apoptosis in DNA-PK –deficient quiescent LSCs and/or BRCA-deficient proliferating LSCs/LPCs from CML-CP/AP, Ph+ B-ALL, AML and ALL patients.

Genetic (Parp1-/-) and pharmacological (olaparib, BMN673) inhibition of PARP1 prolonged survival of mice with CML-CP –like inducible disease and reduced engraftment/prolonged survival of NSG immunodeficient mice with DNA-PK and/or BRCA-deficient primary leukemia (CML-CP, AML and ALL) xenografts in combination with approved drugs.

In conclusion, targeting PARP1 resulted in synthetic lethality in quiescent LSCs and/or proliferating LSCs/LPCs from individual patients identified by GEMA, which display specific defects in DSB repair mechanisms.