Proteomic markers of DNA repair and PI3K pathway activation predict response to the PARP inhibitor BMN 673 in small cell lung cancer

Abstract

Purpose: Small cell lung carcinoma (SCLC) is an aggressive malignancy affecting nearly 30,000 people annually in the United States. We have previously identified elevated PARP1 levels in SCLC and demonstrated in vitro sensitivity to the PARP inhibitors AZD 2281 and AG014699. Here, we evaluate activity of a novel, potent PARP inhibitor, BMN 673, and identify markers of response as a basis for developing predictive markers for clinical application.

Experimental design: Inhibition of SCLC proliferation by BMN 673 was assayed in vitro and effects on tumor growth were measured in SCLC xenograft models. Protein expression and pathway activation was assessed by reverse phase protein array and western blot analysis. PARP inhibition was confirmed using a PAR ELISA.

Results: We demonstrate striking, single agent activity of BMN 673 in SCLC cell lines and xenografts, with single agent BMN 673 exhibiting in vivo activity similar to cisplatin. Sensitivity to BMN 673 was associated with elevated baseline expression levels of several DNA repair proteins, whereas greater drug resistance was observed in SCLC models with baseline activation of the PI3K/mTOR pathway. Furthermore, we developed and confirmed these data with a novel "DNA repair score" consisting of a group of 17 DNA repair proteins.

Conclusions: Elevated expression of multiple DNA repair proteins, as well as a corresponding "DNA repair protein score," predict response to BMN 673 in in vitro SCLC models. These observations complement recent work in which PI3K inhibition sensitizes breast cancer models to PARP inhibition, suggesting cooperation between DNA repair and PI3K pathways.

Figure 1. BMN 673 potently inhibits growth of SCLC in vitro

Proliferation assays using BMN 673 showed SCLC to be exquisitely sensitive to BMN 673 (A). Interestingly the IC50 values of SCLC to BMN 673 and cisplatin indicated a moderate correlation (B).

Figure 2. BMN 673 inhibits SCLC growth in vivo

Animals bearing NCI-H209 and NCI-H1048 flank xenografts treated with BMN 673 showed delayed tumor growth without significant toxicity (A). Lysates prepared from xenografts harvested 2 hours post treatment on day 3 showed decreased poly-ADP ribose (PAR) levels (B) indicating strong inhibition of PARP activity in vivo by BMN 673. (Data presented as mean +/− SEM, *p<0.05, ***p<0.01)

Figure 3. SCLC IC₅₀ to BMN 673 is inversely correlated to DNA repair protein expression

IC₅₀ to BMN correlated to expression of DNA repair proteins (A) demonstrates a strong inverse correlation, as cell lines with higher expression of DNA repair proteins by RPPA are more sensitive to PARP inhibition. DNA repair cluster within the correlation matrix, made up of a group of DNA repair proteins whose expression is highly correlated (B). The correlation to DNA repair is also observed when the “DNA repair score” is applied to the RPPA dataset (C). Proposed model of PARP inhibitor activity in SCLC (D).

Figure 4. PI3K pathway activity correlates to PARP inhibitor resistance

SCLC cell lines with more active PI3K signaling are less sensitive to BMN 673 (A). Similarly, higher pAkt correlates to decreased sensitivity to cisplatin (B).