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.
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.
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.
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.
Small cell lung cancer (SCLC) is one of the most aggressive forms of cancer, with a 5-year survival <7%. A major barrier to progress is the absence of predictive biomarkers for chemotherapy and novel ...targeted agents such as PARP inhibitors. Using a high-throughput, integrated proteomic, transcriptomic, and genomic analysis of SCLC patient-derived xenografts (PDXs) and profiled cell lines, we identified biomarkers of drug sensitivity and determined their prevalence in patient tumors. In contrast to breast and ovarian cancer, PARP inhibitor response was not associated with mutations in homologous recombination (HR) genes (e.g., BRCA1/2) or HRD scores. Instead, we found several proteomic markers that predicted PDX response, including high levels of SLFN11 and E-cadherin and low ATM. SLFN11 and E-cadherin were also significantly associated with in vitro sensitivity to cisplatin and topoisomerase1/2 inhibitors (all commonly used in SCLC). Treatment with cisplatin or PARP inhibitors downregulated SLFN11 and E-cadherin, possibly explaining the rapid development of therapeutic resistance in SCLC. Supporting their functional role, silencing SLFN11 reduced in vitro sensitivity and drug-induced DNA damage; whereas ATM knockdown or pharmacologic inhibition enhanced sensitivity. Notably, SCLC with mesenchymal phenotypes (i.e., loss of E-cadherin and high epithelial-to-mesenchymal transition (EMT) signature scores) displayed striking alterations in expression of miR200 family and key SCLC genes (e.g., NEUROD1, ASCL1, ALDH1A1, MYCL1). Thus, SLFN11, EMT, and ATM mediate therapeutic response in SCLC and warrant further clinical investigation as predictive biomarkers.
Abstract
Small cell lung cancer (SCLC) is an aggressive disease that accounts for 14% of lung cancers. Very little progress has been made towards the treatment of SCLC in the past four decades and ...there are no established biomarkers to predict effective therapies for patients. In other cancers, SLFN11 plays an important role in sensitizing cancer cells to topoisomerase inhibitors, DNA synthesis inhibitors and alkylating agents. Previously, our lab identified an increase in poly (ADP-Ribose) polymerase 1 (PARP1), an enzyme involved in DNA damage repair, in SCLC patients and cell lines. PARP inhibitors demonstrate significant anti-tumor activity in cell line and animal models of SCLC and are currently being tested in clinical trials for SCLC patients. In Ewing sarcoma (EWS), SLFN11 has been proposed as a biomarker of PARP inhibitor response. Because both EWS and SCLC have high PARP levels and respond favorably to PARP inhibition, we hypothesized that SLFN11 may also be a biomarker for drug sensitivity in SCLC. Using SCLC patient tumors and a large panel of molecularly profiled SCLC cell lines, we investigated the expression of SLFN11 in SCLC and its association with in vitro sensitivity to PARP inhibition (olaparib) and chemotherapy. SLFN11 mRNA levels are significantly higher in SCLC patient tumors relative to normal lung tissue (P = 0.005). In a panel of 51 SCLC cell lines, higher SLFN11 protein expression correlates with both cisplatin (P<0.001) and olaparib (PARP inhibitor; P = 0.05) sensitivity. In fact, SLFN11 is the top protein biomarker of cisplatin sensitivity in SCLC cell lines (of 171 proteins measured). Consistent with what has been shown for other cancer types, SLFN11 mRNA expression is also correlated with sensitivity to irinotecan (P = 0.005) and topotecan (P = 0.05) in SCLC, two drugs frequently used to treat this disease. Expression of other SLFN family members does not correlate with drug sensitivity. SLFN11 protein and mRNA levels are concordant (P<0.001) and both demonstrate a bimodal expression pattern in SCLC cell lines which corresponds to cisplatin (protein, P<0.001; mRNA, P = 0.005) and olaparib (mRNA, P = 0.05) sensitive (SLFN11 high) versus resistant (SLFN11 low) groups. In EWS, leukemia, colon, breast and prostate cancers, SLFN11 functions as an ETS transcription factor response gene. However, a panel of 26 ETS transcription factors did not correlate well with SLFN11 or PARP1 mRNA expression or cisplatin sensitivity, suggesting that SLFN11 expression may be regulated in a different manner in SCLC. In summary, SLFN11 is a predictor of sensitivity to chemotherapies routinely used in the treatment of SCLC, including alkylating agents (cisplatin) and topoisomerase inhibitors (irinotecan, topotecan). Moreover, SLFN11 predicts in vitro response to PARP inhibition, which may have important clinical implications given the ongoing clinical trials investigating PARP as a novel therapeutic target for SCLC.
Citation Format: C. Allison Stewart, Pan Tong, Robert Cardnell, Triparna Sen, Fatemah Mina Masrorpour, Youhong Fan, Jing Wang, Lauren Averett Byers. SLFN11 is a biomarker of sensitivity to PARP inhibition and chemotherapy in small cell lung cancer (SCLC). abstract. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3870.
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