ALC1 links chromatin accessibility to PARP inhibitor response in homologous recombination-deficient cells

The response to poly(ADP-ribose) polymerase inhibitors (PARPi) is dictated by homologous recombination (HR) DNA repair and the abundance of lesions that trap PARP enzymes. It remains unclear, however, if the established role of PARP in promoting chromatin accessibility impacts viability in these settings. Using a CRISPR-based screen, we identified the PAR-binding chromatin remodeller ALC1/CHD1L as a key determinant of PARPi toxicity in HR-deficient cells. ALC1 loss reduced viability of breast cancer gene (BRCA)-mutant cells and enhanced sensitivity to PARPi by up to 250-fold, while overcoming several resistance mechanisms. ALC1 deficiency reduced chromatin accessibility concomitant with a decrease in the association of base damage repair factors. This resulted in an accumulation of replication-associated DNA damage, increased PARP trapping and a reliance on HR. These findings establish PAR-dependent chromatin remodelling as a mechanistically distinct aspect of PARPi responses and therapeutic target in HR-deficient cancers.

NF-κB inhibition by dimethylaminoparthenolide radiosensitizes non-small-cell lung carcinoma by blocking DNA double-strand break repair

Despite optimal chemotherapy, radiotherapy (RT), and/or surgery, non-small-cell lung carcinoma (NSCLC) remains the leading cause of cancer-related death in the US and worldwide. Thoracic RT, a mainstay in the treatment of locally advanced NSCLC, is often restricted in efficacy by a therapeutic index limited by sensitivity of tissues surrounding the malignancy. Therefore, radiosensitizers that can improve the therapeutic index are a vital unmet need. Inhibition of the NF-κB pathway is a proposed mechanism of radiosensitization. Here we demonstrate that inhibition of the canonical NF-κB pathway by dimethylaminoparthenolide (DMAPT) radiosensitizes NSCLC by blocking DNA double-strand break (DSB) repair. NF-κB inhibition results in significant impairment of both homologous recombination (HR) and non-homologous end joining (NHEJ), as well as reductions in ionizing radiation (IR)-induced DNA repair biomarkers. NF-κB inhibition by DMAPT shows preclinical potential for further investigation as a NSCLC radiosensitizer.

Abstract 4189: Homologous recombination pathway-based biomarkers for treatment of non-small cell lung cancer with PARP inhibitors

Introduction: Clinical trials examining the addition of PARP inhibitors (PARPi) to treatment regimens for non-small cell lung cancer (NSCLC) are underway. Of note, these trials are not biomarker driven, and so any benefit may be obscured due to heterogeneity of tumor responses. The first FDA approved PARPi, olaparib, was approved specifically for ovarian cancer patients with germline mutations in BRCA1 or 2. These patients have tumors that show homologous recombination deficiency (HRD), a DNA damage repair pathway defect that confers synthetic lethality in the setting of PARPi therapy. Whether HRD may serve a biomarker for PARPi sensitivity in NSCLC, however, is unclear.

Materials and Methods: Based on prior studies, NSCLC cell lines were classified as 1) HR proficient (A549, NCI-H23, NCI-H460, NCI-H522, NCI-H1299), 2) HR deficient due to early defects in the pathway as evidenced by decreased cisplatin-induced RAD51 focus formation (NCI-H1563, NCI-H1915, NCI-H2087, NCI-H2126) or 3) HR deficient due to late defects in the pathway as evidenced by impaired resolution of ionizing radiation (IR) induced RAD51 and γ-H2AX foci (Calu-1, Calu-6, HCC827, NCI-H520, SK-LU-1). NSCLC cells expressing doxycycline-inducible BRCA1 or 2 shRNA were generated by Tet-pLKO-puro lentiviral transduction. Cell viability assays to determine olaparib IC50 values were performed using CellTiter-Glo and MTS. Gene expression data were extracted from published datasets including CCLE, GSE32665 and TCGA, and expression levels of select genes were assayed by RT-qPCR.

Results: BRCA1/2 shRNA knockdown inhibited IR-induced RAD51 focus formation in HR proficient NSCLC cells. This also induced PARPi sensitivity (A549 olaparib IC50 63 µM -> 1.2 µM with BRCA1 and 18 µM -> 3.4 µM with BRCA2 knockdown). Because BRCA alterations are uncommon in NSCLC, however, other HRD biomarkers were explored. There was no statistically significant difference in PARPi sensitivity among cell lines grouped by cisplatin-induced RAD51 focus formation or resolution of IR-induced RAD51 or γ-H2AX foci. BRCA deficient breast and ovarian cancers overexpress POLQ, which drives DNA repair toward non-HR-dependent pathways including alternative end joining. Like these cancers, NSCLC tumors overexpressed POLQ and RAD54L compared to normal lung, p < 0.001. Expression of these two genes correlated highly in multiple datasets, e.g., r² = 0.69 and p < 0.001 in TCGA adenocarcinomas. High RAD54L expression tended to correlate with low olaparib IC50 values, r = -0.56, p = 0.059. NCI-H1299 and SK-LU-1, which showed the highest RAD54L expression, also showed the highest olaparib sensitivity.

Conclusion: Although certain HRD biomarkers including RAD51 focus formation and impaired resolution did not predict NSCLC olaparib sensitivity, other potential biomarkers, such as BRCA1/2 loss of function and elevated RAD54L expression, may serve as potential HRD-related biomarkers.

Citation Format: Peter V. Deraska, Hunter D. Reavis, Shelby Labe, Alan D. D'Andrea, David Kozono. Homologous recombination pathway-based biomarkers for treatment of non-small cell lung cancer with PARP inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4189. doi:10.1158/1538-7445.AM2017-4189

Efficacy of Analgesic Treatments to Manage Children's Postoperative Pain After Laparoscopic Appendectomy: Retrospective Medical Record Review

Knowledge of the effectiveness of multimodal analgesic treatments to manage children's postoperative pain during hospital stays is limited. Our retrospective chart review of a convenience sample of 200 pediatric surgical patients' pain experiences during the first 24 hours after laparoscopic appendectomy demonstrates the benefits of a multimodal analgesic approach. We found that pediatric patients who received perioperative IV ketorolac in addition to opioids reported statistically significantly lower mean pain intensity (n = 134, mean [M] = 2.9, standard deviation [SD] = 1.7) during the first 24 hours after surgery when compared with the pain intensity of patients who did not receive perioperative IV ketorolac (n = 66, M = 3.7, SD = 1.7, t = 3.14, P = .002). Patients who received perioperative IV ketorolac (M = 0.94, SD = 0.71) also received significantly fewer morphine equivalents of postoperative opioids during the first 24 hours after surgery than those who did not (M = 1.21, SD = 0.78, t = 2.41, P = .02). We will use data from these patients to introduce the potential for a personalized medicine approach to postoperative pain.

Abstract 1644: NF-κB inhibitor DMAPT blocks non-homologous end-joining repair of radiation-induced DSBs in NSCLC

Background: Despite optimal multimodality therapy, non-small cell lung carcinoma (NSCLC) remains the leading cause of cancer-related death in the United States. A common limitation is our inability to provide sufficient radiotherapy (RT) to eradicate tumor due to risk of toxicities in surrounding tissues. There is thus an unmet need for radiosensitizers that can improve the therapeutic index. Dimethylaminoparthenolide (DMAPT), an orally bioavailable small molecule NF-κB inhibitor, inhibits repair of ionizing radiation (IR)-induced DNA double strand breaks (DSBs) and increases control of subcutaneous mouse NSCLC xenografts. While our prior work focused on inhibition of homologous recombination as a mechanism for radiosensitization, we sought to characterize the effect of DMAPT on a second major DSB repair pathway, non-homologous end-joining (NHEJ).

Methods: NHEJ was assessed in NSCLC lines using the pEJ reporter and flow cytometry. The NF-κB super repressor (IκBαS32A,S36A) was used as a control. Immunofluorescence and Western blotting were used to assess NHEJ biomarkers including 53BP1, DNA-PKS2056, Ku70/80 and XRCC4. Cell fractionation was performed to assess Ku chromatin binding. Quantitative RT-PCR was performed to assess gene transcription. Ku complexes were purified to identify binding partners.

Results: NSCLC cells treated with IR-sensitizing doses of DMAPT (5-15 μM) or the NF-κB super repressor showed significant decreases in NHEJ. DMAPT increased the persistence of 53BP1 foci, indicating a failure to complete NHEJ. Regardless of exogenous DNA damage, there was reduced Ku70 chromatin binding following DMAPT treatment. DMAPT-treated cells produced fewer distinct IR-induced DNA-PKS2056 foci. Further, there was decreased IR-induced XRCC4 chromatin recruitment, suggesting that repair was impaired prior to ligation. There was no change in Ku70/80 transcription following DMAPT and/or IR. However, Western blotting of purified Ku complexes showed that DMAPT treatment decreased Ku association with RNA binding partners including RPL19. We also observed decreased recruitment of DNA-PKcs to the Ku complex, suggesting decreased Ku affinity for DSBs.

Conclusions: These results indicate that DMAPT radiosensitizes NSCLC by perturbing the binding affinity of Ku to RNA, DNA and its complex binding partners, thus blocking NHEJ. Further mechanistic investigation and analysis of NHEJ biomarkers in vivo is needed to identify the precise mechanism.

Citation Format: Peter V. Deraska, Colin O’Leary, Jean-Bernard Lazaro, Christopher J. Sweeney, Alan D. D’Andrea, David Kozono. NF-κB inhibitor DMAPT blocks non-homologous end-joining repair of radiation-induced DSBs in NSCLC. [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 1644.

Circulating miR-29a and miR-150 correlate with delivered dose during thoracic radiation therapy for non-small cell lung cancer

Background

Risk of normal tissue toxicity limits the amount of thoracic radiation therapy (RT) that can be routinely prescribed to treat non-small cell lung cancer (NSCLC). An early biomarker of response to thoracic RT may provide a way to predict eventual toxicities—such as radiation pneumonitis—during treatment, thereby enabling dose adjustment before the symptomatic onset of late effects. MicroRNAs (miRNAs) were studied as potential serological biomarkers for thoracic RT. As a first step, we sought to identify miRNAs that correlate with delivered dose and standard dosimetric factors.

Methods

We performed miRNA profiling of plasma samples obtained from five patients with Stage IIIA NSCLC at five dose-points each during radical thoracic RT. Candidate miRNAs were then assessed in samples from a separate cohort of 21 NSCLC patients receiving radical thoracic RT. To identify a cellular source of circulating miRNAs, we quantified in vitro miRNA expression intracellularly and within secreted exosomes in five NSCLC and stromal cell lines.

Results

miRNA profiling of the discovery cohort identified ten circulating miRNAs that correlated with delivered RT dose as well as other dosimetric parameters such as lung V20. In the validation cohort, miR-29a-3p and miR-150-5p were reproducibly shown to decrease with increasing radiation dose. Expression of miR-29a-3p and miR-150-5p in secreted exosomes decreased with radiation. This was concomitant with an increase in intracellular levels, suggesting that exosomal export of these miRNAs may be downregulated in both NSCLC and stromal cells in response to radiation.

Conclusions

miR-29a-3p and miR-150-5p were identified as circulating biomarkers that correlated with delivered RT dose. miR-150 has been reported to decrease in the circulation of mammals exposed to radiation while miR-29a has been associated with fibrosis in the human heart, lungs, and kidneys. One may therefore hypothesize that outlier levels of circulating miR-29a-3p and miR-150-5p may eventually help predict unexpected responses to radiation therapy, such as toxicity.

Electronic supplementary material

The online version of this article (doi:10.1186/s13014-016-0636-4) contains supplementary material, which is available to authorized users.