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PDF file - 67K, Genes modulated by tamoxifen but not placebo in an analysis that combined pre- and post-menopausal women.

Supplementary Figure Legends

PDF file - 233K, VHL mutation status in some but not all tumors from Family NCI-1326.

PDF file - 19K, Genes modulated by tamoxifen but not placebo in an analysis restricted to premenopausal women.

PDF file - 42K, RT-PCR primer sequences.

Validation of Pax8-Cre;Vhl;Bap1 mice.

PDF file - 104K

Five years of tamoxifen reduces breast cancer risk by nearly 50% but is associated with significant side effects and toxicities. A better understanding of the direct and indirect effects of tamoxifen in benign breast tissue could elucidate new mechanisms of breast carcinogenesis, suggest novel chemoprevention targets, and provide relevant early response biomarkers for phase II prevention trials. Seventy-three women at increased risk for breast cancer were randomized to tamoxifen (20 mg daily) or placebo for 3 months. Blood and breast tissue samples were collected at baseline and posttreatment. Sixty-nine women completed all study activities (37 tamoxifen and 32 placebo). The selected biomarkers focused on estradiol and IGFs in the blood; DNA methylation and cytology in random periareolar fine-needle aspirates; and tissue morphometry, proliferation, apoptosis, and gene expression (microarray and reverse transcriptase PCR) in the tissue core samples. Tamoxifen downregulated Ets oncogene transcription factor family members ETV4 and ETV5 and reduced breast epithelial cell proliferation independent of CYP2D6 genotypes or effects on estradiol, ESR1, or IGFs. Reduction in proliferation was correlated with downregulation of ETV4 and DNAJC12. Tamoxifen reduced the expression of ETV4- and ETV5-regulated genes implicated in epithelial-stromal interaction and tissue remodeling. Three months of tamoxifen did not affect breast tissue composition, cytologic atypia, preneoplasia, or apoptosis. A plausible mechanism for the chemopreventive effects of tamoxifen is restriction of lobular expansion into stroma through downregulation of ETV4 and ETV5. The human equivalent of murine multipotential progenitor cap cells of terminal end buds may be the primary target. Cancer Prev Res; 4(11); 1852–62. ©2011 AACR.

Supplemental Figure Legends; Supplemental Table Legends

mTOR complex 1 (mTORC1) is implicated in cell growth control and is extensively regulated. We previously reported that in response to hypoxia, mTORC1 is inhibited by the protein regulated in development and DNA damage response 1 (REDD1). REDD1 is upregulated by hypoxia-inducible factor (HIF)-1, and forced REDD1 expression is sufficient to inhibit mTORC1. REDD1-induced mTORC1 inhibition is dependent on a protein complex formed by the tuberous sclerosis complex (TSC)1 and 2 (TSC2) proteins. In clear-cell renal cell carcinoma (ccRCC), the von Hippel-Lindau (VHL) gene is frequently inactivated leading to constitutive activation of HIF-2 and/or HIF-1, which may be expected to upregulate REDD1 and inhibit mTORC1. However, mTORC1 is frequently activated in ccRCC, and mTORC1 inhibitors are effective against this tumor type; a paradox herein examined. REDD1 was upregulated in VHL-deficient ccRCC by in silico microarray analyses, as well as by quantitative real-time PCR, Western blot, and immunohistochemistry. Vhl disruption in a mouse model was sufficient to induce Redd1. Using ccRCC-derived cell lines, we show that REDD1 upregulation in tumors is VHL dependent and that both HIF-1 and HIF-2 are, in a cell-type-dependent manner, recruited to, and essential for, REDD1 induction. Interestingly, whereas mTORC1 is responsive to REDD1 in some tumors, strategies have evolved in others, such as mutations disrupting TSC1, to subvert mTORC1 inhibition by REDD1. Sequencing analyses of 77 ccRCCs for mutations in TSC1, TSC2, and REDD1, using PTEN as a reference, implicate the TSC1 gene, and possibly REDD1, as tumor suppressors in sporadic ccRCC. Understanding how ccRCCs become refractory to REDD1-induced mTORC1 inhibition should shed light into the development of ccRCC and may aid in patient selection for molecular-targeted therapies. Mol Cancer Res; 9(9); 1255–65. ©2011 AACR.

PDF file - 3706K, Pathway Analysis.

Supplemental Figure 1. Elevated NQO1 expression in patients with HNC correlates with poor overall survival to standard therapy; Supplemental Figure 2. Functional shRNA-NQO1 knockdown rescues β-lapinduced cell death; Supplemental Figure 3. β-Lap-induced NQO1 dependent DNA damage and NAD+ depletion; Supplemental Figure 4. Combination sublethal doses of β-lap and low dose IR induce NQO1 dependent anti-cancer lethality; Supplemental Figure 5. Cooperative antitumor efficacy using a combination of IR and β-lap to treat HNC xenograft models; Figure 6. Expression of Ki-67 after combination of β-lap and IR in HNC xenograft models; Supplemental Table 1. NQO1 enzyme activity and abrogation of activity in 41 HNC cell lines and primary human IMR90 fibroblasts; Supplemental Table 2. Equitoxic doses comparing single to combined treatment in HNC cells; Supplemental Table 3. Individual patient gender, age, subsite, stage, histology and IHC scoring for NQO1 and Catalase

PDF file - 201K

PDF file - 37K, Detailed RT-PCR results.

PDF file - 23K, Radiosensitization of normal human astrocytes (NHA) with NVP-BEZ235.

PDF file - 246K, NVP-BEZ235 inhibits the DDR in U87-vIII cells.

RNA-seq results from HBEC-shp53 and HBEC-shp53-PCDH7 cells

PDF file - 650K, NVP-BEZ235 impairs growth of U87-vIII tumors when given in conjunction with IR.

PDF file - 523K, NVP-BEZ235 inhibits the DDR in GBM9 neurospheres.

Purpose:Development of tumor-specific therapies for the treatment of recalcitrant non–small cell lung cancers (NSCLC) is urgently needed. Here, we investigated the ability of β-lapachone (β-lap, ARQ761 in clinical form) to selectively potentiate the effects of ionizing radiation (IR, 1–3 Gy) in NSCLCs that overexpress NAD(P)H:Quinone Oxidoreductase 1 (NQO1).Experimental Design:The mechanism of lethality of low-dose IR in combination with sublethal doses of β-lap was evaluated in NSCLC lines in vitro and validated in subcutaneous and orthotopic xenograft models in vivo. Pharmacokinetics and pharmacodynamics (PK/PD) studies comparing single versus cotreatments were performed to validate therapeutic efficacy and mechanism of action.Results:β-Lap administration after IR treatment hyperactivated PARP, greatly lowered NAD+/ATP levels, and increased double-strand break (DSB) lesions over time in vitro. Radiosensitization of orthotopic, as well as subcutaneous, NSCLCs occurred with high apparent cures (>70%), even though 1/8 β-lap doses reach subcutaneous versus orthotopic tumors. No methemoglobinemia or long-term toxicities were noted in any normal tissues, including mouse liver that expresses the highest level of NQO1 (∼12 units) of any normal tissue. PK/PD responses confirm that IR + β-lap treatments hyperactivate PARP activity, greatly lower NAD+/ATP levels, and dramatically inhibit DSB repair in exposed NQO1+ cancer tissue, whereas low NQO1 levels and high levels of catalase in associated normal tissue were protective.Conclusions:Our data suggest that combination of sublethal doses of β-lap and IR is a viable approach to selectively treat NQO1-overexpressing NSCLC and warrant a clinical trial using low-dose IR + β-lap against patients with NQO1+ NSCLCs.

Supplementary Figures S1-S3; Supplementary Table S1.

Purpose: Carcinogenesis is an adaptive process between nascent tumor cells and their microenvironment, including the modification of inflammatory responses from antitumorigenic to protumorigenic. Radiation exposure can stimulate inflammatory responses that inhibit or promote carcinogenesis. The purpose of this study is to determine the impact of radiation exposure on lung cancer progression in vivo and assess the relevance of this knowledge to human carcinogenesis.Experimental Design: K-rasLA1 mice were irradiated with various doses and dose regimens and then monitored until death. Microarray analyses were performed using Illumina BeadChips on whole lung tissue 70 days after irradiation with a fractionated or acute dose of radiation and compared with age-matched unirradiated controls. Unique group classifiers were derived by comparative genomic analysis of three experimental cohorts. Survival analyses were performed using principal component analysis and k-means clustering on three lung adenocarcinoma, three breast adenocarcinoma, and two lung squamous carcinoma annotated microarray datasets.Results: Radiation exposure accelerates lung cancer progression in the K-rasLA1 lung cancer mouse model with dose fractionation being more permissive for cancer progression. A nonrandom inflammatory signature associated with this progression was elicited from whole lung tissue containing only benign lesions and predicts human lung and breast cancer patient survival across multiple datasets. Immunohistochemical analyses suggest that tumor cells drive predictive signature.Conclusions: These results demonstrate that radiation exposure can cooperate with benign lesions in a transgenic model of cancer by affecting inflammatory pathways, and that clinically relevant similarities exist between human lung and breast carcinogenesis. Clin Cancer Res; 20(6); 1610–22. ©2014 AACR.

Glioblastomas are lethal brain tumors that are treated with conventional radiation (X-rays and gamma rays) or particle radiation (protons and carbon ions). Paradoxically, radiation is also a risk factor for GBM development, raising the possibility that radiotherapy of brain tumors could promote tumor recurrence or trigger secondary gliomas. In this study, we determined whether tumor suppressor losses commonly displayed by patients with GBM confer susceptibility to radiation-induced glioma. Mice with Nestin-Cre-driven deletions of Trp53 and Pten alleles were intracranially irradiated with X-rays or charged particles of increasing atomic number and linear energy transfer (LET). Mice with loss of one allele each of Trp53 and Pten did not develop spontaneous gliomas, but were highly susceptible to radiation-induced gliomagenesis. Tumor development frequency after exposure to high-LET particle radiation was significantly higher compared with X-rays, in accordance with the irreparability of DNA double-strand breaks (DSB) induced by high-LET radiation. All resultant gliomas, regardless of radiation quality, presented histopathologic features of grade IV lesions and harbored populations of cancer stem-like cells with tumor-propagating properties. Furthermore, all tumors displayed concomitant loss of heterozygosity of Trp53 and Pten along with frequent amplification of the Met receptor tyrosine kinase, which conferred a stem cell phenotype to tumor cells. Our results demonstrate that radiation-induced DSBs cooperate with preexisting tumor suppressor losses to generate high-grade gliomas. Moreover, our mouse model can be used for studies on radiation-induced development of GBM and therapeutic strategies.Significance:This study uncovers mechanisms by which ionizing radiation, especially particle radiation, promote GBM development or recurrence.

PDF file - 1617KB, Figure S1. Malignant Characteristics of Invasive Adenocarcinoma in K-rasLA1 Mice; Figure S2. Radiation Effects on the Incidence of Various Endpoints in K-rasLA1 Mice; Figure S3. Comparative Genomic Analyses and Classifier Isolation from Irradiated Versus Unirradiated Control K-rasLA1 Mice; Figure S4. Comparative Genomic Analysis of Whole Lungs Reveals Unique Gene Classifiers Capable of Specifying Individual Experimental Cohorts; Figure S5. Only "Fractionated" Classifier Demonstrates Clinical Relevance for Lung Cancer Patient Survival; Figure S6. "Fractionated" Classifier Capable of Predicting Overall Survival in Patients with Breast, but not Lung Squamous Cell Cancer; Supplementary Figure S7. Cox Regression Analysis Exposes 6 Genes Within "Fractionated" Classifier Which Retain Predictive Capacity; Table S1. Logistic Regression Analysis of Unirradiated K-rasLA1 Mice for Gender and Strain Effects on Various Endpoints; Table S2. Logistic Regression Analysis for Gender and Strain Effects on Various Endpoints Controlling for Experiment; Table S3. Logistic Regression Analysis of Radiation Effects on the Incidence of Invasive Adenocarcinoma Controlling for Gender and Strain; Table S4. Multivariate Cox Analysis for Gender and Strain Effects on Overall Survival Controlling for Experiment; Table S5. Multivariate Cox Analysis of Radiation Effects on Overall Survival Controlling for Gender and Strain Effects; Table S6. IPA Network Annotations Associated with Corresponding Gene Lists.

PDF file - 92K, NVP-BEZ235 does not interfere with the anti-tumor effects of TMZ in U87-vIII tumors.

PDF file - 70K

Supplemental Information

Supplementary Methods, References, and Figure Legends, Supplementary Fig. S1-High magnification images of PCDH7 IHC staining in normal human lung and lung adenocarcinomas. Supplementary Fig. S2-NSCLC tissue microarray analysis of PCDH7 immunoexpression. Supplementary Fig. S3-PCDH7 induces cellular transformation of HBEC cells and induces a gene expression program that promotes cell proliferation. Supplementary Fig. S4-All PCDH7 isoforms induce MAPK signaling in HBEC-shp53-KRASG12V cells. Supplementary Fig. S5-PCDH7 synergizes with mutant EGFR to promote tumor formation. Supplementary Fig. S6-CRISPR/Cas9-mediated inhibition of PCDH7 sensitizes NSCLC cells to MEK and ERK inhibitors. Supplementary Fig. S7-PCDH7 isoforms A, C, and D bind SET in EGFR-mutant cells. Supplementary Fig. S8-SET localization studies in HBECs and NSCLC cells and requirement of SET for PCDH7-induced MAPK pathway activation. Supplementary Fig. S9-Treatment of NSCLC cells with a SET inhibitor FTY720 induces cell death. Supplementary Table S1. Expression and survival analysis of PCDH family members in lung adenocarcinoma. Supplementary Table S2. Affymetrix probe IDs analyzed for each PCDH family member. Supplementary Table S3. Summary of clinical and pathologic information of the cohort of NSCLC patient tissue blocks used for TMA generation. Supplementary Table S4. Analysis of tissue microarray correlations. Supplementary Table S5. Correlation between PCDH7 upregulation and alterations in KRAS or EGFR. Supplementary Table S7. List of antibodies utilized in this study. Supplementary Table S8. List of primer sequences utilized in this study.

Non–small cell lung cancer (NSCLC) is the leading cause of cancer-associated deaths worldwide. Given the efficacy of membrane proteins as therapeutic targets in human malignancies, we examined cell-surface receptors that may act as drivers of lung tumorigenesis. Here, we report that the PROTOCADHERIN PCDH7 is overexpressed frequently in NSCLC tumors where this event is associated with poor clinical outcome. PCDH7 overexpression synergized with EGFR and KRAS to induce MAPK signaling and tumorigenesis. Conversely, PCDH7 depletion suppressed ERK activation, sensitized cells to MEK inhibitors, and reduced tumor growth. PCDH7 potentiated ERK signaling by facilitating interaction of protein phosphatase PP2A with its potent inhibitor, the SET oncoprotein. By establishing an oncogenic role for PCDH7 in lung tumorigenesis, our results provide a rationale to develop novel PCDH7 targeting therapies that act at the cell surface of NSCLC cells to compromise their growth. Cancer Res; 77(1); 187–97. ©2016 AACR.

Figure S1: Cre-mediated excision of floxed alleles and induction of double strand breaks in murine brains. Figure S2: DNA damage in primary astrocytes and murine brains induced by different radiation types. Figure S3: Histopathology and cell lineage markers in radiation-induced gliomas (RIG). Figure S4: Sox2 expression in RIG-derived cell lines and tumor growth kinetics. Figure S5: Loss of p53 and Pten in RIG-derived cell lines. Figure S6: Non-Met amplified RIG. Table S1: List of PCR and RT-PCR primers. Table S2: RIG-derived lines. Table S3: Subcutaneous and orthotopic tumors generated from RIG-derived cell lines. Table S4: A panel of 33 RIGs used for immunohistochemical analysis. Table S5. List of GISTIC hits.

Purpose: Pancreatic cancer is the fourth leading cause of cancer-related deaths, in which the 5-year survival rate is less than 5%. Current standard of care therapies offer little selectivity and high toxicity. Novel, tumor-selective approaches are desperately needed. Although prior work suggested that β-lapachone (β-lap) could be used for the treatment of pancreatic cancers, the lack of knowledge of the compound's mechanism of action prevented optimal use of this agent.Experimental Design: We examined the role of NAD(P)H:quinone oxidoreductase-1 (NQO1) in β-lap–mediated antitumor activity, using a series of MIA PaCa-2 pancreatic cancer clones varying in NQO1 levels by stable shRNA knockdown. The antitumor efficacy of β-lap was determined using an optimal hydroxypropyl-β-cyclodextran (HPβ-CD) vehicle formulation in metastatic pancreatic cancer models.Results: β-Lap–mediated cell death required ∼90 enzymatic units of NQO1. Essential downstream mediators of lethality were as follows: (i) reactive oxygen species (ROS); (ii) single-strand DNA breaks induced by ROS; (iii) poly(ADP-ribose)polymerase-1 (PARP1) hyperactivation; (iv) dramatic NAD+/ATP depletion; and (v) programmed necrosis. We showed that 1 regimen of β-lap therapy (5 treatments every other day) efficaciously regressed and reduced human pancreatic tumor burden and dramatically extended the survival of athymic mice, using metastatic pancreatic cancer models.Conclusions: Because NQO1 enzyme activities are easily measured and commonly overexpressed (i.e., >70%) in pancreatic cancers 5- to 10-fold above normal tissue, strategies using β-lap to efficaciously treat pancreatic cancers are indicated. On the basis of optimal drug formulation and efficacious antitumor efficacy, such a therapy should be extremely safe and not accompanied with normal tissue toxicity or hemolytic anemia. Clin Cancer Res; 17(2); 275–85. ©2011 AACR.

The clinical experimental agent, β-lapachone (β-lap; Arq 501), can act as a potent radiosensitizer in vitro through an unknown mechanism. In this study, we analyzed the mechanism to determine whether β-lap may warrant clinical evaluation as a radiosensitizer. β-Lap killed prostate cancer cells by NAD(P)H:quinone oxidoreductase 1 (NQO1) metabolic bioactivation, triggering a massive induction of reactive oxygen species, irreversible DNA single-strand breaks (SSB), poly(ADP-ribose) polymerase-1 (PARP-1) hyperactivation, NAD+/ATP depletion, and μ-calpain–induced programmed necrosis. In combination with ionizing radiation (IR), β-lap radiosensitized NQO1+ prostate cancer cells under conditions where nontoxic doses of either agent alone achieved threshold levels of SSBs required for hyperactivation of PARP-1. Combination therapy significantly elevated SSB level, γ-H2AX foci formation, and poly(ADP-ribosylation) of PARP-1, which were associated with ATP loss and induction of μ-calpain–induced programmed cell death. Radiosensitization by β-lap was blocked by the NQO1 inhibitor dicoumarol or the PARP-1 inhibitor DPQ. In a mouse xenograft model of prostate cancer, β-lap synergized with IR to promote antitumor efficacy. NQO1 levels were elevated in ∼60% of human prostate tumors evaluated relative to adjacent normal tissue, where β-lap might be efficacious alone or in combination with radiation. Our findings offer a rationale for the clinical utilization of β-lap (Arq 501) as a radiosensitizer in prostate cancers that overexpress NQO1, offering a potentially synergistic targeting strategy to exploit PARP-1 hyperactivation. Cancer Res; 70(20); 8088–96. ©2010 AACR.

It is poorly understood how driver mutations in cancer genes work together to promote tumor development. Renal cell carcinoma (RCC) offers a unique opportunity to study complex relationships among cancer genes. The four most commonly mutated genes in RCC of clear-cell type (the most common type) are two-hit tumor suppressor genes, and they cluster in a 43-Mb region on chromosome 3p that is deleted in approximately 90% of tumors: VHL (mutated in ∼80%), PBRM1 (∼50%), BAP1 (∼15%), and SETD2 (∼15%). Meta-analyses that we conducted show that mutations in PBRM1 and SETD2 co-occur in tumors at a frequency higher than expected by chance alone, indicating that these mutations may cooperate in tumorigenesis. In contrast, consistent with our previous results, mutations in PBRM1 and BAP1 tend to be mutually exclusive. Mutation exclusivity analyses (often confounded by lack of statistical power) raise the possibility of functional redundancy. However, mutation exclusivity may indicate negative genetic interactions, as proposed herein for PBRM1 and BAP1, and mutations in these genes define RCC with different pathologic features, gene expression profiles, and outcomes. Negative genetic interactions among cancer genes point toward broader context dependencies of cancer gene action beyond tissue dependencies. An enhanced understanding of cancer gene dependencies may help to unravel vulnerabilities that can be exploited therapeutically. Cancer Res; 73(14); 4173–9. ©2013 AACR.

PDF file, 87K, Cooperation and antagonism among cancer genes: the renal cancer paradigm. Supplementary Figure 1. Kaplan-Meier curves of overall survival for tumors with mutations in PBRM1 and SETD2.

Supplementary Figure 6 from Prostate Cancer Radiosensitization through Poly(ADP-Ribose) Polymerase-1 Hyperactivation

The development of new modes of diagnosis and targeted therapy for lung cancer is dependent on the identification of unique cell surface features on cancer cells and isolation of reagents that bind with high affinity and specificity to these biomarkers. We recently isolated a 20-mer peptide which binds to the lung adenocarcinoma cell line, H2009, from a phage-displayed peptide library. We show here that the cellular receptor for this peptide, TP H2009.1, is the uniquely expressed integrin, αvβ6, and the peptide binding to lung cancer cell lines correlates to integrin expression. The peptide is able to mediate cell-specific uptake of a fluorescent nanoparticle via this receptor. Expression of αvβ6 was assessed on 311 human lung cancer samples. The expression of this integrin is widespread in early-stage nonsmall cell lung carcinoma (NSCLC). Log-rank test and Cox regression analyses show that expression of this integrin is significantly associated with poor patient outcome. Preferential expression is observed in the tumors compared with the surrounding normal lung tissue. Our data indicate that αvβ6 is a prognostic biomarker for NSCLC and may serve as a receptor for targeted therapies. Thus, cell-specific peptides isolated from phage biopanning can be used for the discovery of cell surface biomarkers, emphasizing the utility of peptide libraries to probe the surface of a cell. [Cancer Res 2007;67(12):5889–95]