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PDF file - 40K, Gene cluster, ER, PR and p53 status of the various HER2+ breast cancer cell lines ((3) and COSMIC database)

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PDF file - 25K, Homologous recombination repair capacity in MCF7 cells

PDF file - 93K, Verification of the expected effects of p65 or IkappaBalpha overexpression on NFkappaB transcriptional activity in breast cancer cells

PDF file - 26K, Lapatinib induces a homologous recombination repair defect in HER2+ breast cancer cell

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HER2 overexpression in breast cancer confers increased tumor aggressiveness. Although anti-HER2 therapies have improved patient outcome, resistance ultimately occurs. PARP inhibitors target homologous recombination (HR)-deficient tumors, such as the BRCA-associated breast and ovarian cancers. In this study, we show that HER2+ breast cancers are susceptible to PARP inhibition independent of an HR deficiency. HER2 overexpression in HER2 negative breast cancer cells was sufficient to render cells susceptible to the PARP inhibitors ABT-888 and AZD-2281 both in vitro and in vivo, which was abrogated by HER2 reduction. In addition, ABT-888 significantly inhibited NF-κB (p65/RelA) transcriptional activity in HER2+ but not HER2 negative breast cancer cells. This corresponded with a reduction in phosphorylated p65 and total IKKα levels, with a concomitant increase in IκBα. Overexpression of p65 abrogated cellular sensitivity to ABT-888, whereas IκBα overexpression reduced cell viability to a similar extent as ABT-888. Therefore, susceptibility of HER2+ breast cancer cells to PARP inhibition may be because of inhibition of NF-κB signaling driven by HER2. Our findings indicate that PARP inhibitors may be a novel therapeutic strategy for sporadic HER2+ breast cancer patients. Cancer Res; 72(18); 4796–806. ©2012 AACR.

PDF file - 62K, MCF7 HER2 cells but not its isogenic MCF7 NEO controls are susceptible to the PARP inhibitors ABT-888 and AZD-2281

PDF file - 45K, ABT-888 reduces levels of the NFkappaB regulated protein cMyc

In men with advanced penile squamous cell carcinoma receiving first-line chemotherapy, visceral metastases (VM) and Eastern Cooperative Oncology Group performance status ≥1 are poor prognostic factors for overall survival (OS). We hypothesized that tumor gene expression profiling may enhance prognostic stratification and identify potential therapeutic targets. In this retrospective study, RNA extracted from macrodissected tumors underwent profiling for the expression of 738 genes using NanoString. Univariate and multivariate analyses assessed the association of genes, VM, and performance status with OS. Tumors were available from 25 men who received first-line cisplatin-based chemotherapy. In univariate analysis, upregulated MAML2 ( p =0.004), KITLG ( p ≤0.0001), and JAK1 ( p =0.029) genes were associated with poor OS, and upregulated FANCA was associated with better OS ( p =0.024). In stepwise multivariate analyses, VM (hazard ratio=12.75, p =0.0001) and MAML2 (hazard ratio=10.411, p =0.003) were associated with poor OS. The presence of none, one, and both of these poor risk factors was associated with significantly different median OS of 18.4 mo, 7.2 mo, and 2.1 mo, respectively. Unsupervised clustering demonstrated two major molecular subtypes with trend for different survivals ( p =0.052). Validation of results is necessary. Patient summary The expression of the MAML2 gene in penile cancers from men receiving first-line cisplatin-based chemotherapy predicted overall survival independent of clinical factors.

Kinases are therapeutically actionable targets. Kinase inhibitors targeting vascular endothelial growth factor receptors (VEGFR) and mammalian target of rapamycin (mTOR) improve outcomes in metastatic clear cell renal cell carcinoma (ccRCC), but are not curative. Metastatic tumor tissue has not been comprehensively studied for kinase gene expression. Paired intra-patient kinase gene expression analysis in primary tumor (T), matched normal kidney (N) and metastatic tumor tissue (M) may assist in identifying drivers of metastasis and prioritizing therapeutic targets. We compared the expression of 519 kinase genes using NanoString in T, N and M in 35 patients to discover genes over-expressed in M compared to T and N tissue. RNA-seq data derived from ccRCC tumors in The Cancer Genome Atlas (TCGA) were used to demonstrate differential expression of genes in primary tumor tissue from patients that had metastasis at baseline (n = 79) compared to those that did not develop metastasis for at least 2 years (n = 187). Functional analysis was conducted to identify key signaling pathways by using Ingenuity Pathway Analysis. Of 10 kinase genes overexpressed in metastases compared to primary tumor in the discovery cohort, 9 genes were also differentially expressed in TCGA primary tumors with metastasis at baseline compared to primary tumors without metastasis for at least 2 years: EPHB2, AURKA, GSG2, IKBKE, MELK, CSK, CHEK2, CDC7 and MAP3K8; p

Intracranial lipomas are rare, but 45% of them occur along the midline cisterns between the hemispheres and are often associated with corpus callosum hypoplasia and craniofacial defects. They are difficult to detect, as they are generally asymptomatic and visible by MRI or by postmortem examination. The exact cause of these interhemispheric lipomas is not known, but they arise from a developmental defect resulting in the maldifferentiation of mesenchymal cells into mesodermal derivatives that are not normally present. We have identified a new mouse mutant called tuft, exhibiting a forebrain, intracranial lipoma with midline craniofacial defects resembling frontonasal dysplasia (FND) that arose spontaneously in our wild-type 3H1 colony. The tuft trait appears to be transmitted in recessive fashion, but approximately 80% less frequent than the expected Mendelian 25%, due to either incomplete penetrance or prenatal lethality. MRI and histological analysis revealed that the intracranial lipoma occurred between the hemispheres and often protruded through the sagittal suture. We also observed a lesion at the lamina terminalis that may indicate improper closure of the anterior neuropore. We have mapped the tuft trait to within an 18 cM region on mouse chromosome 10 by microsatellite linkage analysis and identified several candidate genes involved with craniofacial development and cellular differentiation of adipose tissue. tuft is the only known mouse model for midline craniofacial defects with an intracranial lipoma. Identifying the gene(s) and mutation(s) causing this early developmental defect will help us understand the pathogenesis of FND and related craniofacial disorders.

A large body of evidence shows that p16(INK4a) overexpression predicts improved survival and increased radiosensitivity in HPV-mediated oropharyngeal squamous cell carcinomas.(OPSCC). Here we demonstrate that the presence of transcriptionally active HPV16 in oral cavity squamous cell carcinomas does not correlate with p16(INK4a) overexpression, enhanced local tumor immunity, or improved outcome. It is interesting that HPV-mediated oropharyngeal squamous cell carcinomas can be categorized as having a 'nonaggressive' invasion phenotype, whereas aggressive invasion phenotypes are more common in HPV-negative squamous cell carcinomas. We have developed primary cancer cell lines from resections with known pattern of invasion as determined by our validated risk model. Given that cell lines derived from HPV-mediated oropharyngeal squamous cell carcinomas are less invasive than their HPV-negative counterparts, we tested the hypothesis that viral oncoproteins E6, E7, and p16(INK4a) can affect tumor invasion. Here we demonstrate that p16(INK4a) overexpression in two cancer cell lines (UAB-3 and UAB-4), derived from oral cavity squamous cell carcinomas with the most aggressive invasive phenotype (worst pattern of invasion type 5 (WPOI-5)), dramatically decreases tumor invasiveness by altering expression of extracellular matrix remodeling genes. Pathway analysis integrating changes in RNA expression and kinase activities reveals different potential p16(INK4a)-sensitive pathways. Overexpressing p16(INK4a) in UAB-3 increases EGFR activity and increases MMP1 and MMP3 expression, possibly through STAT3 activation. Overexpressing p16(INK4a) in UAB-4 decreases PDGFR gene expression and reduces MMP1 and MMP3, possibly through STAT3 inactivation. Alternatively, ZAP70/Syk might increase MUC1 phosphorylation, leading to the observed decreased MMP1 expression.

Background: Epidermal growth factor receptor (EGFR) overexpression is present in 80-100% of head and neck cancers, and targeting EGFR with cetuximab has improved outcomes when combined with radiotherapy (XRT). However, over half of these patients still succumb to this disease, necessitating novel therapies. Checkpoint kinase 1 and 2 (Chk1/2) are serine/threonine kinases that prevent cell cycle progression and serve as critical regulators of the DNA-damage response. LY2606368 monomesylate monohydrate (CHKi), a potent inhibitor of Chk1/2, exhibits single agent activity in tumors of squamous cell histology, including head and neck. Because of the role of Chk1/2 in DNA damage response, we hypothesized that CHKi may enhance the cytotoxicity induced by cetuximab and XRT in head and neck cancer. Methods: The HPV-negative UM-SCC1 and HPV-positive UM-SCC47 head and neck cancer cells were used. Doses of drug compounds are as follows: CHKi (LY2606368, Eli Lilly) 1nM; Cetuximab 0.25μg/mL. Cell proliferation was assessed using a Beckman Coulter Counter. Clonogenic survival was measured with colony formation assays. Apoptosis was analyzed using Annexin V-FITC staining and western blot analysis for cleaved and full length caspase-3 and 9. DNA damage and checkpoint signaling was investigated via western blot analysis for phospho- and total Chk1, Chk2, ATM, ATR, and γ-H2AX. Animal studies were performed using orthotopic tongue injection of UM-SCC1-Luc or heterotopic flank injection of UM-SCC47 cells in athymic nude mice, which were then subjected to 3 cycles of once-weekly CHKi (4mg/kg), cetuximab (0.1mg), and 2Gy XRT. Results: The addition of CHKi to cetuximab and XRT resulted in the greatest reduction of cell proliferation and increased cytotoxicity in both HPV positive (HPV+) UM-SCC47 and HPV negative (HPV-) UM-SCC1 cancer cells in vitro. Triple combination treatment effectively reduced cell growth by ∼89% in UM-SCC1 and ∼63% in UM-SCC47 at 96hrs compared to untreated cells. A robust decrease in clonogenic survival in both cell lines was also observed (approximately 90% at 2Gy). Furthermore, this combination abrogated the DNA damage checkpoints induced by cetuximab and XRT, resulting in persistent DNA damage and activation of apoptosis. Specifically, we observed CHKi-mediated downregulation of total and phospho- Chk1, Chk2, ATR, and ATM, with concomitant increases in cleaved caspase-3 and caspase-9. Importantly, combining CHKi, cetuximab, and XRT led to a significant tumor growth delay in mice bearing orthotopic or heterotopic head and neck tumor xenografts compared to control mice. Additionally, no significant weight loss or toxicity was observed in the treatment. Conclusions: CHKi enhanced the in vitro and in vivo cytotoxicity of cetuximab and XRT against human head and neck tumor models. A clinical trial to test this treatment for head and neck cancer patients is underway (NCT02555644). Citation Format: Ling Zeng, Reena Beggs, Tiffiny Cooper, Eddy Shih-Hsin Yang. Combining Chk1/2 inhibition with cetuximab and irradiation enhances in vitro and in vivo cytotoxicity of head and neck cancer models. [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 3046.

Few therapeutic options exist for the highly aggressive triple negative breast cancers (TNBCs). In this study, we report that a contextual synthetic lethality can be achieved both in vitro and in vivo with combined EGFR and PARP inhibition with lapatinib and ABT-888, respectively. The mechanism involves a transient DNA double strand break repair deficit induced by lapatinib and subsequent activation of the intrinsic pathway of apoptosis. Further dissection of the mechanism reveals that EGFR and BRCA1 can be found in the same protein complex, which is reduced by lapatinib. Interestingly, lapatinib also increases cytosolic BRCA1 and EGFR, away from their nuclear DNA repair substrates. Taken together, these results reveal a novel regulation of homologous recombination repair involving EGFR and BRCA1 interaction and alteration of subcellular localization. Additionally, a contextual synthetic lethality may exist between combined EGFR and PARP inhibitors.

HER2 overexpression in breast cancer confers increased tumor aggressiveness. Although anti-HER2 therapies have improved patient outcome, resistance ultimately occurs. PARP inhibitors target homologous recombination (HR)-deficient tumors, such as the BRCA-associated breast and ovarian cancers. In this study, we show that HER2+ breast cancers are susceptible to PARP inhibition independent of an HR deficiency. HER2 overexpression in HER2 negative breast cancer cells was sufficient to render cells susceptible to the PARP inhibitors ABT-888 and AZD-2281 both in vitro and in vivo, which was abrogated by HER2 reduction. In addition, ABT-888 significantly inhibited NF-κB (p65/RelA) transcriptional activity in HER2+ but not HER2 negative breast cancer cells. This corresponded with a reduction in phosphorylated p65 and total IKKα levels, with a concomitant increase in IκBα. Overexpression of p65 abrogated cellular sensitivity to ABT-888, whereas IκBα overexpression reduced cell viability to a similar extent as ABT-888. Therefore, susceptibility of HER2+ breast cancer cells to PARP inhibition may be because of inhibition of NF-κB signaling driven by HER2. Our findings indicate that PARP inhibitors may be a novel therapeutic strategy for sporadic HER2+ breast cancer patients. Cancer Res; 72(18); 4796–806. ©2012 AACR.

Background: Overexpression of HER2 in breast cancer is associated with aggressive tumor features and poor patient survival. Current therapeutic agents targeting this receptor have increased the survival rate of patients with HER2+ breast cancer; however some patients eventually develop resistance to these therapies. We have previously reported that HER2+ breast cancers are susceptible to poly (ADP-Ribose) polymerase inhibitors (PARPi) alone independent of a basal or induced DNA repair deficiency but instead via suppression of NF-κB signaling. In this study, we investigated PARPi sensitivity in HER2+ breast cancer cells that are resistant to the HER2 targeted agent trastuzumab. Materials and Methods: HER2+ breast cancer cell lines BT-474, UACC812, SKBRR3 and their trastuzumab resistant counterparts were used in this study. Cells were treated with vehicle or 10µM ABT-888 or transfected with scrambled or PARP1 siRNA. NF-κB transcriptional activity was measured using a NF-κB-driven luciferase reporter assay. Protein expression was measured by Western blot analysis. Cellular cytotoxicity and viability following PARPi was assessed with colony formation and ATPlite assays, respectively. Results: HER2+ parent and trastuzumab resistant breast cancer cells showed similar susceptibility to the PARPi ABT-888. There was a dose response reduction in survival fraction (greater than 70% at 10μM) and a greater than 40% decrease in cell viability with 10μM ABT-888. This cytotoxicity was associated with more than 50% attenuation of NF-κB transcriptional activity and reduced expression of the NF-κB activator IKKα. Suppression of NF-κB signaling was also observed utilizing PARP1 siRNA. Conclusions: HER2+ breast cancer cells resistant to trastuzumab continue to be sensitive to PARP inhibition through attenuation of the NF-κB signaling pathway. These results support the use of PARPi as part of a therapeutic strategy for patients with HER2+ breast cancer. Citation Format: Monica E. Wielgos, Tiffiny Cooper, Andres Forero, James A. Bonner, Francisco J. Esteva, C K. Osborne, Rachel Schiff, Albert F. LoBuglio, Eddy S. Yang. Trastuzumab resistant HER2+ breast cancer cells retain sensitivity to poly (ADP-ribose) polymerase (PARP) inhibition. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5469. doi:10.1158/1538-7445.AM2014-5469

Background/Objectives: Few therapeutic options are effective for triple negative breast cancers (TNBCs) necessitating novel approaches. We previously reported a novel synthetic lethality with combined EGFR and PARP inhibition due to a homologous recombination (HR) repair defect induced EGFR inhibition. The mechanism of the HR deficiency involved disruption of EGFR/BRCA1 interaction and sequestration of EGFR and BRCA1 to the cytosol. In this study, we have extended these findings to encompass multiple subtypes of triple negative breast cancer and EGFR inhibitors. Additionally, we further investigated the mechanisms by which EGFR regulates HR DNA repair. Methods: TNBC cells, including MDA-MB-231 (mesenchymal stem-like), MDA-MB-468 (basal-like), HCC1187 (immunomodulatory), BT549 (mesenchymal), MDA-MB-453 (luminal androgen receptor), were assessed for cytotoxicity and cell viability following EGFR inhibition (lapatinib, erlotinib, or cetuximab), PARP inhibition, or both by colony formation or ATPlite assays. MALDI-TOF mass spectroscopy was utilized to ascertain protein-protein interaction. To confirm interaction data and determine subcellular location we utilized immunoprecipitation and subcellular fractionation. To determine if interactions were dependent on DNA, lysates were treated with Ethidium Bromide and DNAse prior to immunoprecipitation. Results: EGFR inhibition with lapatinib, cetuximab, or erlotinib induced a contextual synthetic lethality with the PARP inhibitor, veliparib, in vitro in multiple TNBC subtypes, including MDA-MB-231 (mesenchymal stem-like), MDA-MB-468 (basal-like), HCC1187 (immunomodulatory), BT549 (mesenchymal), MDA-MB-453 (luminal androgen receptor). Interestingly, mass spectroscopy reaffirmed EGFR interaction with BRCA1 but also identified a novel interaction between EGFR and PARP1. These interactions were not found upon EGFR inhibition with lapatinib. Furthermore, we validated with immunoprecipitation and in vitro protein binding assays EGFR, BRCA1, and PARP1 protein-protein interactions that were disrupted upon EGFR inhibition. Additionally, these proteins were found to interact in the nucleus, independent of DNA. Lastly, EGFR inhibition also reduced nuclear EGFR and BRCA1 without significant changes in PARP1 localization. Conclusions: These results reveal a contextual synthetic lethality between combined EGFR and PARP inhibition in multiple subtypes of TNBC, suggesting potential generalizability of this combination in patients with TNBC. Furthermore understanding the mechanism by which EGFR regulates DNA repair may provide novel targets to confer other contextual synthetic lethalities that may be exploited to treat the aggressive TNBCs. Citation Format: Jennifer Anne Stanley, Somaira Nowsheen, Tiffiny Cooper, Andres Forero, Alfred LoBuglio, Eddy Yang. Contextual synthetic lethality in human triple negative breast cancer cells involving a novel interaction between DNA repair proteins EGFR, PARP1, and BRCA1. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5471. doi:10.1158/1538-7445.AM2014-5471

Purpose: The human papilloma virus (HPV) has recently become a prevalent cause of human head and neck cancer (HNC), which often exhibits dysregulated epidermal growth factor receptor (EGFR) signaling. We previously reported that in non-HPV-associated HNC, inhibition of EGFR (EGFRi) attenuates DNA double stranded break (DSB) repair and subsequently sensitizes tumors to inhibitors of poly (ADP-ribose) polymerase (PARP), which target DNA repair deficient tumors. Because patients with HPV-associated HNC have been shown to exhibit increased sensitivity to DNA damage, we evaluated the response of HPV (+) HNC cells to combination EGFRi and PARPi compared to HPV (-) HNC cells. Methods: HPV (-) UM-SCC1 and UM-SCC6, as well as HPV (+) SCC-47 and SCC-90 were utilized for in vitro studies. Cell growth and survival fraction were evaluated via cell proliferation and colony formation assays, respectively. DNA damage studies were performed using standard γ-H2AX and Rad51 foci. Lastly, in vivo studies were conducted in mice bearing HNC tumor xenografts as well as a human tumor explant from a lymph node metastasis of a HPV(+) HNC patient. Results: Interestingly, HPV (+) HNCs exhibited the greatest sensitivity both in vitro and in vivo to PARP inhibition alone. This correlated with a blunted DNA damage response. In contrast, HPV (-) HNCs were most sensitive to combination EGFRi/PARPi, which correlated with persistent DNA damage. Conclusions: HPV(+) head and neck cancers may be sensitive to PARP inhibition alone. Our in vitro and in vivo results warrant further testing of PARP inhibitors as part of therapy for HNCs. Citation Format: Tiffiny Cooper, Marcela Rodriguez, Hoa Q. Trummell, Alice Weaver, James A. Bonner, Eddy S. Yang. PARP inhibition in HPV positive head and neck cancers. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 635. doi:10.1158/1538-7445.AM2013-635

Purpose: Dysregulation of the epidermal growth factor receptor (EGFR) family is a hallmark of many cancers. Although targeting of EGFR family has improved outcomes, many patients ultimately fail this therapy. PARP inhibitors (PARPi) have gained recent attention due to their unique selectivity in killing homologous recombination (HR)-deficient tumors while maintaining minimal toxicity in normal tissues. We have previously shown that EGFR inhibition induces synthetic lethality with PARPi in head and neck squamous cell carcinomas (HNSCCs) in vitro by attenuating DNA repair pathways. In this study, we validated these observations in vivo in HNSCCs xenografts. Importantly, we also tested this strategy in other EGFR dysregulated cancers. Methods: Cervical, breast, and head and neck cancer cell lines were used in this study. DNA damage and repair were assessed by immunofluorescence staining of cells for γ-H2AX, Rad51, and DNA-Pk foci and/or chromosomally integrated HR and nonhomologous end-joining based GFP reporter assays. Cell viability was determined via colony formation and ATPlite assays. Tumor growth delay was assessed in mice bearing tumor xenografts. Results: Combined EGFR and PARP inhibition resulted in the greatest tumor growth delay versus either agent alone in mice bearing head and neck tumor xenografts (9 week tumor growth delay when compared to PARPi alone, 3 week tumor growth delay when compared to EGFR inhibitor alone). This correlated with persistent γ-H2AX foci indicative of unresolved DNA damage. Interestingly, this combination was also effective in other EGFR dysregulated tumors. Human cervical and breast cancer cells exhibited enhanced cytotoxicity with EGFR and PARP inhibition compared to either agent alone (80-99% cytotoxicity with combination vs 0-20% with either agent alone). Similar to head and neck cancer, susceptibility to PARPi induced by EGFR inhibition was associated with deficient NHEJ- and HR-mediated DNA repair and subsequent persistence of DNA damage. Conclusions: Thus, by generating a DNA repair deficit, EGFR inhibition can induce synthetic lethality with PARP inhibition. This can be an innovative treatment strategy for tumors with dysregulated EGFR signaling. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4684. doi:1538-7445.AM2012-4684