Using consistent terms in precision medicine to eliminate patient confusion

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Background: Biomarker testing has advanced precision medicine in cancer. However, not all eligible patients benefit from biomarker-driven therapies due to suboptimal testing rates. A working group of 20 patient advocacy groups representing solid/hematologic malignancies, three professional societies, and 18 pharmaceutical and diagnostics companies identified patient confusion inconsistent testing terms as a possible contributing factor to biomarker testing underutilization. The group aimed to address patients’ confusion by identifying and adopting consistent, plain language terms for biomarker and germline genetic testing that are applicable across cancer types. Methods: Following a stakeholder roundtable discussion on barriers to precision medicine, working group members participated in interviews on their goals for consistent testing terminology for their constituents. We then conducted a framework analysis covering five themes: available testing by cancer type; purpose of test; biospecimen source; terms used in patient education; and preferred plain language term. Working group members were surveyed on preferences for germline testing terminology and also deployed a preliminary patient survey to their constituents to gain insight on preferences for germline testing terms. Results: Interviews, framework analysis, and surveys revealed notable differences across cancer communities. We identified at least 33 different terms related to biomarker, genetic and genomic testing being used in patient education and clinical care among the different cancer communities and stakeholders. Terminology was complicated by the variety of testing modalities and gene mutations tested for across cancers. Following multiple discussions, working group members agreed on two umbrella terms to distinguish between somatic and germline testing with additional context for specific cancer communities. “Biomarker testing” was selected as the somatic testing term. “Genetic testing for an inherited mutation” and “genetic testing for inherited cancer risk” were selected as preferred germline testing terms. Conclusions: Our findings highlight the disparate testing terminology landscape and the need for consistent terms to reduce patient confusion, improve communication, facilitate shared decision-making and assure concordance in policy development.

Comprehensive genomic sequencing of paired ovarian cancers reveals discordance in genes that determine clinical trial eligibility

OBJECTIVE

We analyzed comprehensive genomic sequencing results from paired ovarian cancer samples to identify changes in mutational events over time.

METHODS

DNA from paired FFPE tumor samples from 50 ovarian cancer patients in the Clearity Foundation Data Repository was analyzed for genomic mutations (GM), copy number alterations (CNA), microsatellite status (MS), tumor mutation burden (TMB), and loss of heterozygosity (LOH) by hybrid-capture, next-generation sequencing of up to 315 genes. Genomic profiles were compared between samples from the same patient. Poor quality results excluded 6 pairs from all analyses and 9 from CNA or LOH.

RESULTS

Forty-four patients with predominantly advanced stage disease (34, 77%) and serous histology (31, 70%) received a median of 3 intervening treatment regimens (range 1-13). Analysis of 22 primary and recurrent sample pairs and 22 recurrent tumor pairs detected a median of 2 GM (range 0-5) and 1 CNA (range 0-6)/sample. TMB, MS, and LOH results were mostly concordant across paired samples. GM were consistent across most pairs [32/44 (73%) concordant], while CNA concordance was less [18/35 (51%)]. No changes were detected in therapeutically relevant GM, but 23% of patients had GM or CNA in the second sample that affect clinical trial eligibility.

CONCLUSIONS

Paired ovarian cancer samples demonstrate stable genomic alterations across time. However, discordance was observed for some genes used as eligibility criteria for molecularly targeted clinical trials. Repeat tumor testing may be useful in cases where eligibility for such trials is deemed important after consideration of testing costs and potential clinical benefit.

Constitutively active ESR1 mutations in gynecologic malignancies and clinical response to estrogen-receptor directed therapies

OBJECTIVE

Endocrine therapy is often considered as a treatment for hormone-responsive gynecologic malignancies. In breast cancer, activating mutations in the estrogen receptor (mutESR1) contribute to therapeutic resistance to endocrine therapy, especially aromatase inhibitors (AIs). The purpose of this study was to evaluate the frequency and clinical relevance of ESR1 genomic alterations in gynecologic malignancies.

METHODS

DNA from FFPE tumor tissue obtained during routine clinical care for 9645 gynecologic malignancies (ovary, fallopian tube, uterus, cervix, vagina, vulvar, and placenta) was analyzed for all classes of genomic alterations (base substitutions (muts), insertions, deletions, rearrangements, and amplifications) in ESR1 by hybrid capture next generation sequencing. A subset of alterations was characterized in laboratory-based transcription assays for response to endocrine therapies.

RESULTS

A total of 295 ESR1 genomic alterations were identified in 285 (3.0%) cases. mutESR1 were present in 86 (0.9%) cases and were more common in uterine compared to other cancers (2.0% vs <1%, respectively p < 0.001). mutESR1 were enriched in carcinomas with endometrioid versus serous histology (4.4% vs 0.2% respectively, p < 0.0001 in uterine and 3.5% vs 0.3% respectively, p = 0.0004 in ovarian carcinomas). In three of four patients with serial sampling, mutESR1 emerged under the selective pressure of AI therapy. Despite decreased potency of estrogen receptor (ER) antagonists in transcriptional assays, clinical benefit was observed following treatment with selective ER-targeted therapy, in one case lasting >48 months.

CONCLUSIONS

While the prevalence of ESR1 mutations in gynecologic malignancies is low, there are significant clinical implications useful in guiding therapeutic approaches for these cancers.

Change in Topoisomerase 1-Positive Circulating Tumor Cells Affects Overall Survival in Patients with Advanced Breast Cancer after Treatment with Etirinotecan Pegol

Purpose: Preplanned exploratory analyses were performed to identify biomarkers in circulating tumor cells (CTC) predictive of response to the topoisomerase 1 inhibitor etirinotecan pegol (EP).Experimental Design: The BEACON trial treated patients with metastatic breast cancer (MBC) with EP or treatment of physician's choice (TPC). Blood from 656 of 852 patients (77%) was processed with ApoStream to enrich for CTCs. A multiplex immunofluorescence assay measured expression of candidate response biomarkers [topoisomerase 1 (Top1), topoisomerase 2 (Top2), Ki67, RAD51, ABCG2, γH2AX, and terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL)] in CTCs. Patients were classified as Top1 low (Top1Lo) or Top1 high (Top1Hi) based on median CTC Top1 expression. Correlation of CTC biomarker expression at baseline, cycle 2 day 1 (C2D1), and cycle 4 day 1 with overall survival (OS) was investigated using Cox regression and Kaplan-Meier analyses.Results: Overall, 98% of samples were successfully processed, of which 97% had detectable CTCs (median, 47-63 CTCs/mL; range, 0-2,020 CTCs/mL). Top1, Top2, and TUNEL expression was detected in 52% to 90% of samples; no significant associations with OS were observed in pretreatment samples for either group. EP-treated patients with low C2D1Top1⁺ CTCs had improved OS compared with those with higher positivity (14.1 months vs. 11.0 months, respectively; HR, 0.7; P = 0.02); this difference was not seen in TPC-treated patients (HR, 1.12; P = 0.48). Patients whose CTCs decreased from Top1Hi to Top1Lo at C2D1 had the greatest OS benefit from EP (HR, 0.57; P = 0.01).Conclusions: CTC Top1 expression following EP treatment may identify patients with MBC most likely to have an OS benefit. Clin Cancer Res; 24(14); 3348-57. ©2018 AACR.

Abstract 58: Differences in genomic alterations revealed by sequencing of 182 genes in recurrent ovarian cancer specimens compared to TCGA analysis: rearrangements in PTCH1 and FLT3; high frequency of RAS pathway alteration

Recent comprehensive genomic analyses of advanced stage, high grade serous ovarian carcinomas carried out by TCGA (Nature 274: 609-615, 2011) have revealed their heterogeneous nature and provide an explanation for the failure of molecularly targeted drugs evaluated without consideration of the tumor molecular characteristics of the patients treated. Copy number (CN) alterations or mutations in RB, RAS-MAPK, and PI3K-AKT pathway genes occur in ∼35%, 20%, and 35% of the tumors, respectively. Activation of these pathways may confer sensitivity to drugs that target them (e.g., PI3K or AKT inhibitors, MEK inhibitors, CDK inhibitors) as well as resistance to drugs (e.g., HER2 or EGFR inhibitors) that have failed in ovarian cancer clinical trials. A comprehensive evaluation of the genetic aberrations in targetable pathways can therefore inform the selection of appropriate drugs and combinations for each patient in the context of clinical trials.

As part of molecular profiling analyses performed for recurrent ovarian cancer patients to inform selection of their next treatment, the presence of mutations or alterations (e.g., CN changes) in 182 genes that encode proteins that are key mediators in oncogenic and tumor suppressive pathways were determined using a validated exon-capture sequencing platform provided in a CLIA-certified laboratory setting. 20 serous (4 primary/16 recurrent) and 4 recurrent mixed or pure clear cell ovarian tumor samples were analyzed. A median of 2.5 (range 0-7) alterations were detected in the serous histology specimens; frequencies of p53 mutations (16; 80%) and amplifications in CCND1 (1; 5%), CCND2 (1; 5%), CCNE1 (2; 10%) are consistent with those observed in the TCGA tumors. In contrast, more frequent RAS pathway aberrations (45% vs. 20%) corresponding to KRAS amplification (3;15%) and mutations/truncations in NF1 (5; 20%) or NF2 (1; 5%) were observed, possibly reflecting the recurrent nature of these samples (TCGA used primary tumors). Only one PIK3CA amplification was detected (i.e.,

5%) in contrast to the 18% observed in the TCGA dataset. Amplifications of IGF1R (3; 15%) and ERBB2 (1;5%) were also detected in the serous histology tumors, while PIK3CA and KRAS mutations were only detected in the tumors with mixed cc and endometrioid histologies. Interestingly, a predicted protein-truncating rearrangement in PTCH1 and a kinase-activating exon duplication in FLT3 were detected in tumors from single patients suggesting drugs targeting the HH pathway and FLT3 as options for ovarian cancer patients.

While it is important to increase the number of samples analyzed, these data suggest that selection of patients for clinical trials should be informed by comprehensive molecular characterization of recurrent tumor specimens.

Citation Format: Deborah A. Zajchowski, Doron Lipson, Gary Palmer, Laura K. Shawver. Differences in genomic alterations revealed by sequencing of 182 genes in recurrent ovarian cancer specimens compared to TCGA analysis: rearrangements in PTCH1 and FLT3; high frequency of RAS pathway alteration. [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 58. doi:10.1158/1538-7445.AM2013-58

Proliferation pathway aberration frequencies in BRCA1- and BRCA2-mutated ovarian cancers

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Background: Large-scale genomic analyses of high-grade, advanced-stage serous ovarian cancers by The Cancer Genome Atlas (TCGA) project revealed aberrations in genes comprising key proliferation and survival pathways (RB-E2F, RAS, PI3K) in the majority of tumors. Patients with germline BRCA1/2-mutations have more favorable prognoses than non-BRCA carriers, and recent work suggests that BRCA2 carriers do better than BRCA1. We hypothesized that concurrent proliferation pathway aberrations and BRCA1/2 mutations in tumors might play a role in patient outcome. Methods: Mutation, copy number, and clinical data for 309 TCGA-profiled serous ovarian tumors were downloaded from the MSKCC cBIO web portal. Each tumor was scored as aberrant for a pathway if any gene (RB: RB1, CDKN2A, CCND1, CCND2, E2F3, CCNE1; PI3K: PIK3CA, PTEN, AKT1, AKT2; RAS: KRAS, BRAF, NF1) in that pathway was mutated, amplified, or deleted. Results: 205 of 309 tumors had an aberration in at least one of these pathways. The frequency of pathway alteration differed significantly in BRCA1 (82%, 28/34), BRCA2 (52%, 17/33) and BRCA1/2 WT (66%, 160/242) tumors (BRCA1 vs. BRCA2: Fisher’s p= 0.0096). BRCA1 tumors more frequently contained alterations in multiple pathways than BRCA2 or WT tumors (41% vs. 24% or 25%, respectively). RB-E2F pathway alteration frequency was significantly different (BRCA1: 56%, BRCA2: 18%, WT: 43%, p=0.0043), but no significant differences in PI3K and RAS pathway aberration frequencies (BRCA1%: 41, 38; BRCA2%: 36, 27; WT% 28, 27), respectively, were observed. In agreement with the previous report, BRCA2 patients had significantly better overall survival (OS) than either BRCA1 or WT patients (median OS months for BRCA1: 35.9, BRCA2 45.4, BRCA1/2 WT 27.8; p=0.001). Presence of pathway alterations was not significantly associated with OS in BRCA1, BRCA2, or WT patients in this cohort. Conclusions: These results show a negative association between BRCA2 mutations and aberrations in key proliferation and survival pathways. Beyond BRCA1 and BRCA2 genetic mutations, the elevated frequency of pathway alteration in BRCA1 vs. BRCA2 tumors highlights differences that may be important for patient prognosis as well as therapy responses.

Correlation of tumor-profiling results with drug selection in ovarian cancer patients

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Background: With the aim of informing therapy-selection decisions for ovarian cancer patients, we have profiled tumors from 190 ovarian cancer patients since 2008 for expression of 25 biomarkers associated with drug response. For 48 patients with mature follow-up data, we asked how frequently the drugs designated as likely to be of clinical benefit based on the tumor profile were administered. Methods: The tumor profiles and therapeutic choices of 48 patients that received a median of 2 (range 1-9) prior therapies for recurrent disease were extracted from our privacy-protected database. Protein levels of drug sensitivity (ER/PR, hormonal agents; TOPO1, topotecan/irinotecan (T-I); TOP2A, liposomal doxorubicin/etoposide (PLD-E); SPARC, nab-paclitaxel, N-P) and resistance (TS, pemetrexed/capecitabine (PC); RRM1, gemcitabine (G)) markers in each tumor were compared to expression in the ovarian cancer population to assign drugs likely to be associated with clinical benefit (values ≥ 25th percentile: sensitivity; ≤ 25th percentile: resistance). Results: A median of two drugs (range 1-5) were prioritized for each patient based on marker expression. 38 patients received one of the 6 drug classes evaluated by the profile. Of those 38, 22 (58%) received a therapy that correlated with the profile and 16 (42%) received drugs that were not prioritized by the profile. G and PLD were most frequently administered both before (68%) and after (48%) profiling but were supported by the tumor profile in only 40% (4/10: G) and 30% (3/10: PLD-E) of the cases. These frequencies are similar to the patient fraction (26-34%) in which those drugs were each prioritized by profiling, suggesting that the profile is not influencing therapy choice. In contrast, 11 of the 14 patients who received N-P, T-I, or hormonal agents had tumor profiles that prioritized those agents, a frequency of profile match to the treatment received that is higher than expected based on the patient fraction assigned to each therapy. Conclusions: These results require confirmation in a much larger study, but suggest that tumor profiling may guide clinical decision-making for some therapies, although frequently used drugs are often given regardless of the tumor profiling evidence.

Abstract 5077: Molecular profiling in recurrent ovarian cancer patients: Considerations for the design of clinical studies to validate profiling for therapy selection

Therapies for recurrent, advanced stage ovarian cancer are often empirically selected and associated with similarly poor response rates and short progression-free survivals. Our ultimate goal is to improve patient outcomes by enabling a more rational selection of chemotherapies based upon individual tumor molecular profiles. To identify molecular markers to include in such profiling, we performed a literature search for evidence supporting the association between chemotherapy response markers and in vivo responses to drugs currently employed in ovarian cancer treatment. We found multiple reports that demonstrated a correlation between expression levels of RRM1, TOPO1, TOPO2, ERCC1, TS, MGMT, SPARC, MRP1, MDR1, or BCRP and clinical responses to gemcitabine, topoisomerase 1 and 2 inhibitors, platinum, fluoropyrimidines, temozolamide, nab-paclitaxel, taxanes, and other drugs. However, few studies addressed the correlation between these biomarkers and therapy responses for ovarian cancer patients. We therefore measured expression of these markers in formalin-fixed, paraffin-embedded tumor blocks (obtained following informed patient consent) by immunohistochemical analyses at CLIA-certified laboratories to establish expression characteristics of these proteins in epithelial ovarian carcinomas. Protein expression data were recorded as histoscores (% tumor cells stained x intensity). We profiled fifty-nine advanced stage ovarian, peritoneal, or fallopian tube cancers of which 42 were of either serous papillary histology or adenocarcinomas (25 primary and 17 recurrent serous ovarian tumor specimens). The first-line response to platinum-taxane therapy for most of these patients (23 sensitive, 7 resistant, 2 refractory) and BRCA1 and 2 mutation status (7 BRCA1 mutation carriers) were also known. Most of the marker proteins were heterogeneously expressed both within the tumor sample and across the cohort of patient tumors. The exceptions were TOPO2 and MDR1, which were poorly detected in most tumors. Interestingly, primary specimens had significantly lower expression levels of MDR1 and higher expression of RRM1 and TOPO1 than recurrent lesions underscoring the potential importance of determining the molecular profile of recurrent specimens. Six of the seven BRCA1 mutation carriers were sensitive to platinum-taxane treatment, but no significant association with platinum responsiveness was observed for expression of any of the measured proteins. These data provide a basis for establishing expression cutoff points for each marker to test hypotheses that correlate individual or combined marker expression profiles with responses to chemotherapy in prospective analyses. Profiling of recurrent specimens is recommended for future clinical trials to evaluate this approach to individualize cancer therapy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5077. doi:10.1158/1538-7445.AM2011-5077

Abstract 809: Selecting ovarian cancer patients for clinical trials using a broad panel of molecular markers

Our understanding of the molecular biology of ovarian cancer is rapidly expanding, in part through efforts such as The Cancer Genome Atlas (TCGA) project, which is comprehensively cataloguing the genomic aberrations of 500 advanced serous ovarian carcinomas. These and other studies have shown that ovarian cancers are molecularly complex and highly heterogeneous. Importantly, the prevalence of over-expression or alteration of any one drug target is very low in ovarian cancer (with the exception of p53 mutations, which occur in 70-90% of advanced stage serous carcinomas). Therefore, the identification of patients for clinical trials of targeted drug therapies by measuring expression of a single target or pathway has limited usefulness. To improve the efficiency of trial enrollment and also the likelihood of successful therapeutic outcomes, we propose to evaluate every patient using a broad tumor marker panel. In feasibility studies, we have analyzed ovarian tumors for a panel of markers that includes molecular targets such as EGFR, HER2, VEGF, PDGFR, IGF1R, c-met, c-kit, ER, and AR, as well as signaling pathway proteins (e.g., HIF1alpha, COX2, PTEN). Because targeted agents are frequently combined with chemotherapy in ovarian cancer clinical trials, we also included proteins associated with response to representative agents (e.g., platinums, taxanes, anthracyclines), such as drug transporters (BCRP, MRP1, PGP) and proteins involved in DNA repair/modification (ERCC1, MGMT) or synthesis (TS, RRM1, TOPO1/2A). Formalin-fixed, paraffin-embedded tumor blocks were obtained following patient consent and protein expression was measured by immunohistochemical analyses at CLIA-certified laboratories. Expression data were recorded as histoscores (% tumor cells stained x intensity). To date, 44 tumor specimens (histology: 28 serous, 6 clear cell, 1 endometrioid, 1 MMMT, and 2 granulosa cell; 3 stage I, 3 stage II, 31 stage III, 2 stage IV, 5 unknown) have been profiled. Approximately half of the specimens were derived from the ovary; the others were recurrent lesions or metastases (peritoneum, pelvis, omentum, liver, and colon) discovered at diagnosis. Two were pleural effusion or lung nodule biopsies. The markedly heterogeneous nature of ovarian tumors is apparent from the results of this analysis. One exception is the expression of the angiogenic factor VEGF, which is highly expressed in &gt;80% of these tumors. PDGFR alpha and beta were highly co-expressed in multiple tumors. IGF1R was highly expressed in ∼25%, ER alpha in ∼40%, and AR in ∼20% of ovarian tumors. No tumor over-expressed HER2 and EGFR was highly detected in only 10% of the cases. Importantly, hierarchical clustering analyses based upon drug target expression revealed the existence of several sub-groups of ovarian cancer patients and provide clues to select from treatment options.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 809.

The ubiquitin-conjugating enzyme E2-EPF is overexpressed in primary breast cancer and modulates sensitivity to topoisomerase II inhibition

We identified the ubiquitin-conjugating enzyme E2-EPF mRNA as differentially expressed in breast tumors relative to normal tissues and performed studies to elucidate its putative role in cancer. We demonstrated that overexpression of E2-EPF protein correlated with estrogen receptor (ER) negativity in breast cancer specimens and that its expression is cell cycle-regulated, suggesting a potential function for E2-EPF in cell cycle progression. However, reduction of E2-EPF protein levels by > 80% using RNAi had no significant effects on the proliferation of HeLa cervical cancer cells or ER(-) MDA-MB-231 or MDA-MB-453 breast cancer cells. Because E2-EPF protein levels were elevated during the G(2)/M phase of the cell cycle and because E2-EPF mRNA in tumor specimens was frequently coexpressed with genes involved in cell cycle control, spindle assembly, and mitotic surveillance, the possibility that E2-EPF might have a function in the cellular response to agents that induce a G(2) checkpoint or an M checkpoint was investigated. E2-EPF knockdown sensitized HeLa cells to the topoisomerase (topo) II inhibitors etoposide and doxorubicin and also increased topo IIalpha protein levels. These data suggest that combined administration of topo II-directed drugs and E2-EPF inhibitors may enhance their clinical effectiveness.

Anti-EphA2 antibodies decrease EphA2 protein levels in murine CT26 colorectal and human MDA-231 breast tumors but do not inhibit tumor growth

The EphA2 receptor tyrosine kinase has been shown to be over-expressed in cancer and a monoclonal antibody (mAb) that activates and down-modulates EphA2 was reported to inhibit the growth of human breast and lung tumor xenografts in nude mice. Reduction of EphA2 levels by treatment with anti-EphA2 siRNA also inhibited tumor growth, suggesting that the anti-tumor effects of these agents are mediated by decreasing the levels of EphA2. As these studies employed human tumor xenograft models in nude mice with reagents whose cross reactivity with murine EphA2 is unknown, we generated a mAb (Ab20) that preferentially binds, activates, and induces the degradation of murine EphA2. Treatment of established murine CT26 colorectal tumors with Ab20 reduced EphA2 protein levels to approximately 12% of control tumor levels, yet had no effect on tumor growth. CT26 tumor cell colonization of the lung was also not affected by Ab20 administration despite having barely detectable levels of EphA2. We also generated and tested a potent agonistic mAb against human EphA2 (1G9-H7). No inhibition of humanMDA-231 breast tumor xenograft growth was observed despite evidence for >85% reduction of EphA2 protein levels in the tumors. These results suggest that molecular characteristics of the tumors in addition to EphA2 over-expression may be important for predicting responsiveness to EphA2-directed therapies.

Anti-tumor efficacy of the nucleoside analog 1-(2-deoxy-2-fluoro-4-thio-?-D-arabinofuranosyl) cytosine (4?-thio-FAC) in human pancreatic and ovarian tumor xenograft models

1-(2-deoxy-2-fluoro-4-thio-beta-D-arabinofuranosyl) cytosine (4'-thio-FAC) is a deoxycytidine analog that has been shown previously to have impressive anti-proliferative and cytotoxic effects in vitro and in vivo toward colorectal and gastric tumors. In our present studies, the pharmacokinetic behavior in nude mice and the effectiveness of 4'-thio-FAC against human pancreatic and ovarian tumor growth were assessed in comparison with standard chemotherapeutic agents. Potent in vitro anti-proliferative effects were observed against pancreatic (Capan-1, MIA-PaCa-2, BxPC-3) and ovarian (SK-OV-3, OVCAR-3, ES-2) cancer cell lines with IC(50) of 0.01-0.2 microM. In vivo anti-tumor activity was evaluated in nude mice bearing subcutaneously (s.c.) implanted human pancreatic tumor xenografts or intraperitoneally (i.p.) disseminated human ovarian xenografted tumors. Oral daily administration of 4'-thio-FAC for 8-10 days significantly inhibited the growth of gemcitabine-resistant BxPC-3 pancreatic tumors and induced regression of gemcitabine-refractory Capan-1 tumors. 4'-Thio-FAC was also a highly effective inhibitor of ovarian peritoneal carcinomatosis. In the SK-OV-3 and ES-2 ovarian cancer models, 4'-thio-FAC prolonged survival to a greater extent than that observed with gemcitabine. Furthermore, the superiority of 4'-thio-FAC to carboplatin and paclitaxel was demonstrated in the ES-2 clear cell ovarian carcinoma model. Studies provide evidence that 4'-thio-FAC is a promising new alternative to gemcitabine and other chemotherapeutic drugs in the treatment of a variety of tumor indications, including pancreatic and ovarian carcinoma.

Multiplex gene expression analysis for high-throughput drug discovery: screening and analysis of compounds affecting genes overexpressed in cancer cells

Drug discovery strategies are needed that can rapidly exploit multiple therapeutic targets associated with the complex gene expression changes that characterize a polygenic disease such as cancer. We report a new cell-based high-throughput technology for screening chemical libraries against several potential cancer target genes in parallel. Multiplex gene expression (MGE) analysis provides direct and quantitative measurement of multiple endogenous mRNAs using a multiplexed detection system coupled to reverse transcription-PCR. A multiplex assay for six genes overexpressed in cancer cells was used to screen 9000 chemicals and known drugs in the human prostate cancer cell line PC-3. Active compounds that modulated gene expression levels were identified, and IC50 values were determined for compounds that bind DNA, cell surface receptors, and components of intracellular signaling pathways. A class of steroids related to the cardiac glycosides was identified that potently inhibited the plasma membrane Na(+)K(+)-ATPase resulting in the inhibition of four of the prostate target genes including transcription factors Hoxb-13, hPSE/PDEF, hepatocyte nuclear factor-3alpha, and the inhibitor of apoptosis, survivin. Representative compounds selectively induced apoptosis in PC-3 cells compared with the nonmetastatic cell line BPH-1. The multiplex assay distinguished potencies among structural variants, enabling structure-activity analysis suitable for chemical optimization studies. A second multiplex assay for five toxicological markers, Hsp70, Gadd153, Gadd45, O6-methylguanine-DNA methyltransferase, and cyclophilin, detected compounds that caused DNA damage and cellular stress and was a more sensitive and specific indicator of potential toxicity than measurement of cell viability. MGE analysis facilitates rapid drug screening and compound optimization, the simultaneous measurement of toxicological end points, and gene function analysis.

Identification of gene expression profiles that predict the aggressive behavior of breast cancer cells

With the goal of identifying genes that have an expression pattern that can facilitate the diagnosis of primary breast cancers (BCs) as well as the discovery of novel drug leads for BC treatment, we used cDNA hybridization arrays to analyze the gene expression profiles (GEPs) of nine weakly invasive and four highly invasive BC cell lines. Differences in gene expression between weakly and highly invasive BC cells were identified that enabled the definition of consensus GEPs for each invasive phenotype. To determine whether the consensus GEPs, comprising 24 genes, could be used to predict the aggressiveness of previously uncharacterized cells, gene expression levels and comparative invasive and migratory characteristics of nine additional human mammary epithelial cell strains/lines were determined. The results demonstrated that the GEP of a cell line is predictive of its invasive and migratory behavior, as manifest by the morphology of its colonies when cultured on a matrix of basement membrane constituents (i.e., Matrigel). We found that the expression of keratin 19 was consistently elevated in the less aggressive BC cell lines and that vimentin and fos-related antigen-1 (FRA-1) were consistently overexpressed in the more highly aggressive BC cells. Moreover, even without these three genes, the GEP of a cell line still accurately predicted the aggressiveness of the BC cell, indicating that the expression pattern of multiple genes may be used as BC prognosticators because single markers often fail to be predictive in clinical specimens.

Identification of selective estrogen receptor modulators by their gene expression fingerprints

Clinical studies have shown that estrogen replacement therapy (ERT) reduces the incidence and severity of osteoporosis and cardiovascular disease in postmenopausal women. However, long term estrogen treatment also increases the risk of endometrial and breast cancer. The selective estrogen receptor (ER) modulators (SERMs) tamoxifen and raloxifene, cause antagonistic and agonistic responses when bound to the ER. Their predominantly antagonistic actions in the mammary gland form the rationale for their therapeutic utility in estrogen-responsive breast cancer, while their agonistic estrogen-like effects in bone and the cardiovascular system make them candidates for ERT regimens. Of these two SERMs, raloxifene is preferred because it has markedly less uterine-stimulatory activity than either estrogen or tamoxifen. To identify additional SERMs, a method to classify compounds based on differential gene expression modulation was developed. By analysis of 24 different combinations of genes and cells, a selected set of assays that permitted discrimination between estrogen, tamoxifen, raloxifene, and the pure ER antagonist ICI164384 was generated. This assay panel was employed to measure the activity of 38 compounds, and the gene expression fingerprints (GEFs) obtained for each compound were used to classify all compounds into eight groups. The compound's GEF predicted its uterine-stimulatory activity. One group of compounds was evaluated for activity in attenuating bone loss in ovariectomized rats. Most compounds with similar GEFs had similar in vivo activities, thereby suggesting that GEF-based screens could be useful in predicting a compound's in vivo pharmacological profile.

Proteinase inhibitor 9, an inhibitor of granzyme B-mediated apoptosis, is a primary estrogen-inducible gene in human liver cells

Although liver is an estrogen target tissue, the number of hepatic genes known to be directly induced by estrogen is very small. We identified proteinase inhibitor 9, or PI-9, as being rapidly and strongly induced by estrogen in an estrogen receptor-positive human liver cell line (HepG2-ER7). Since PI-9 mRNA was also induced by estrogen in a human liver biopsy sample, PI-9 is a genuine estrogen-regulated human gene. PI-9 is a potent inhibitor of granzyme B and of granzyme B-mediated apoptosis. Estrogens induced PI-9 mRNA within 2 h, PI-9 mRNA levels reached a plateau of 30-40-fold induction in 4 h, and induction was not blocked by cycloheximide, indicating that induction of PI-9 mRNA is a primary response. The antiestrogen trans-hydroxytamoxifen was a partial agonist for PI-9 mRNA induction, whereas the antiestrogen ICI 182, 780 was a pure antagonist. Western blot analysis showed that estrogen strongly increases PI-9 protein levels. Inhibition of transcription with actinomycin D resulted in identical rates of PI-9 mRNA decay in the presence and absence of estrogen. We isolated genomic clones containing the PI-9 promoter region, identified a putative transcription start site, and carried out transient transfections of PI-9-luciferase reporter gene constructs. The estrogen, moxestrol, elicited a robust induction from the PI-9-luciferase reporter. Mutational inactivation of three potential imperfect estrogen response elements in the PI-9 5'-flanking region had no effect on moxestrol estrogen receptor induction.

Estrogen modulation of apolipoprotein(a) expression. Identification of a regulatory element

Elevated plasma levels of the lipoprotein particle Lp(a) are a major risk factor for cardiovascular disease. Lp(a) plasma levels are determined by the level of expression of its characteristic protein component, apo(a). Apo(a) expression is modulated by several hormones, of which estrogens are the best known. The chromosomal region responsible for estrogen response was identified within an apo(a) enhancer located at approximately 26 kilobases from the apo(a) promoter. Although the estrogen-responsive unit contains a potential estrogen response element, binding of estrogen receptor-alpha to DNA was not necessary. The receptor, activated by bound estradiol, interacts through its transactivation domains with a transcription factor necessary for the function of the enhancer, preventing its binding to DNA.

Protein fold analysis of the B30.2-like domain

The B30.2-like domain occurs in some members of a diverse and growing family of proteins containing zinc-binding B-box motifs, whose functions include regulation of cell growth and differentiation. The B30.2-like domain is also found in proteins without the zinc-binding motifs, such as butyrophilin (a transmembrane glycoprotein) and stonustoxin (a secreted cytolytic toxin). Currently, the function for the B30.2-like domain is not clear and the structure of a protein containing this domain has not been solved. The secondary structure prediction methods indicate that the B30.2-like domain consists of fifteen or fewer beta-strands. Fold recognition methods identified different structural topologies for the B30.2-like domains. Secondary structure prediction, deletion and lack of local sequence identity at the C-terminal region for certain members of the family, and packing of known core structures suggest that a structure containing two beta domains is the most probable of these folds. The most C-terminal sequence motif predicted to be a beta-strand in all B30.2-like domains is a potential subdomain boundary based on the sequence-structure alignments. Models of the B30.2-like domains were built based on immunoglobulin-like folds identified by the fold recognition methods to evaluate the possibility of the B30.2 domain adopting known folds and infer putative functional sites. The SPRY domain has been identified as a subdomain within the B30.2-like domain. If the B30.2-like domain is a subclass of the SPRY domain family, then this analysis would suggest that the SPRY domains are members of the immunoglobulin superfamily.

The novel estrogen-responsive B-box protein (EBBP) gene is tamoxifen-regulated in cells expressing an estrogen receptor DNA-binding domain mutant

We have identified a 2.6-kb mRNA whose steady state levels are increased 2- to 4-fold by treatment of human mammary epithelial cells (HMEC) stably expressing an estrogen receptor (ER) transgene with either estrogen (E) or the antiestrogen, 4-hydroxy-tamoxifen (HT). The cDNA corresponding to this mRNA encodes a 564-amino acid protein, named estrogen-responsive B box protein (EBBP), that is a new member of a subfamily within the B box zinc finger protein family, which includes transcription factors (e.g. TIF1), tumor suppressor proteins (e.g. PML), and proteins implicated in development (e.g. ret finger protein, XNF7). The EBBP mRNA is detectable by Northern blot analysis in most tissues, with the exception of liver and peripheral blood lymphocytes, and the gene has been mapped to human chromosome 17p11.2. In contrast to most B box family members, EBBP has a predominantly cytoplasmic localization. Studies of the estrogenic regulation of EBBP expression demonstrated that the E-dependent increase in EBBP mRNA levels in the ER-transfected HMEC is an early, ER-mediated, and cycloheximide-insensitive process. In HMEC stably transfected with an ER mutant containing a deletion in the second zinc finger of the DNA-binding domain, E and HT had different effects on EBBP gene expression; EBBP regulation by E was dramatically reduced while the effects of HT were augmented. These data indicate that HT can modulate EBBP mRNA expression through a mutated ER, which has little activity when bound by E, and suggest that different molecular mechanisms control the E and HT responsiveness of the EBBP gene.

Different estrogen receptor structural domains are required for estrogen- and tamoxifen-dependent anti-proliferative activity in human mammary epithelial cells expressing an exogenous estrogen receptor

Estrogen (E) inhibits the growth of both non-tumorigenic, immortal human mammary epithelial cells (HMEC) and breast cancer cells which stably express exogenous estrogen receptors (ER). The anti-estrogenic compounds 4-hydroxy-tamoxifen (HT) and ICI 164384 (ICI) have different effects on the growth of the ER-transfectants. HT is a potent growth inhibitor, while ICI has no effect by itself but is able to block the anti-proliferative effects of E and HT. In order to elucidate the mechanism by which E or HT-bound ER inhibit cell growth, we have evaluated the effects of these compounds on the growth of HMEC stably expressing ER with mutations or deletions in the N-terminal A/B domain, the DNA-binding domain (DBD), and the C-terminal ligand-binding domain. These studies revealed that E and HT require different structural domains of the ER for their anti-proliferative activities. The N-terminal A/B domain is required for HT-, but not E-dependent growth inhibition. The DNA-binding domain of the ER is not essential for HT-mediated anti-proliferative effects, but is important for E-dependent activity. The effect of ER mutations on the ligand-inducible expression of the endogenous progesterone receptor (PR) and pS2 genes was also evaluated. Neither gene was induced in the cells containing the ER mutated in the DBD, even though cell growth was inhibited. These results suggest that E and HT use different pathways to elicit their anti-proliferative effects and that this occurs via modulation of genes that are controlled by mechanisms different from those important for activation of the PR and pS2 genes.

Estrogen inhibits the growth of estrogen receptor-negative, but not estrogen receptor-positive, human mammary epithelial cells expressing a recombinant estrogen receptor

Estrogen is essential for the growth of the normal mammary gland and most estrogen receptor (ER)-positive mammary carcinomas. To better understand the differences between the estrogen response pathways in normal and tumor cells, we have stably transfected ER-negative immortal, nontumorigenic human mammary epithelial cells and ER-negative breast cancer cells with an ER-encoding expression vector. Unexpectedly, estrogen treatment (1.0 nM) inhibited the proliferation of ER-transfected nontumorigenic and tumor-derived cells. The control transfectants and parental cells exhibited no response to estrogen concentrations as high as 1.0 microM. This inhibitory effect was attributed to a decreased growth rate and a perturbation of the cell cycle distribution by estrogen treatment of the ER transfectants. The inhibitory response was blocked by cotreatment with the antiestrogen ICI 164,384 as predicted for a pure antagonist of estrogen action. However, treatment with the antiestrogen hydroxytamoxifen caused growth inhibition, implying that hydroxytamoxifen acts as an agonist of estrogen action in ER-transfected cells. Since estrogen is a mitogenic and not a growth-inhibitory stimulus for ER-positive breast cancers and cell lines, we tested the effect of constitutive, high level expression of the ER in ER-positive tumor cells. Stable transfection of ER-positive MCF-7 and T47D cells with the ER expression vector yielded cells with varying amounts of ER. At ER levels comparable to those found in the ER-negative transfected cells, the MCF-7 and T47D ER transfectants were not inhibited by estrogen. These data suggest that ER-positive breast cancer cells can tolerate higher constitutive levels of ER expression than ER-negative cells. The mechanism by which this is accomplished may be an essential step in the process which yields ER-positive tumors.

Induction of estrogen-regulated genes differs in immortal and tumorigenic human mammary epithelial cells expressing a recombinant estrogen receptor

Studies on estrogen receptor (ER)-positive human breast cancer cell lines have shown that estrogen treatment positively modulates the expression of the genes encoding transforming growth factor-alpha (TGF alpha), 52-kDa cathepsin-D, and pS2. To determine whether these genes would be similarly regulated by estrogens in normal human mammary epithelial cells, we stably transfected immortal nontumorigenic human mammary epithelial cells with an ER-encoding expression vector. ER-negative tumor cells were also transfected for comparison. Levels of TGF alpha and 52-kDa cathepsin-D mRNA were enhanced by estrogen treatment of both ER-transfected immortal and tumorigenic cells, demonstrating that the ER by itself is sufficient to elicit estrogenic regulation of the expression of these genes. In contrast, expression of the pS2 gene was detected only in the ER-transfected tumor cells. The ER in both cell lines is capable of recognizing the pS2 promoter, however, since estrogen enhanced the activity of an introduced pS2-CAT reporter plasmid in transient expression analyses. These and other experiments with somatic cell hybrids between the immortal cells and ER+/pS2+ MCF-7 tumor cells, where pS2 gene expression is extinguished, support the conclusion that the immortal nontumorigenic cells encode gene products that block endogenous pS2 expression. These results also imply that such repressors are not active in the tumor cells.

Suppression of tumor-forming ability and related traits in MCF-7 human breast cancer cells by fusion with immortal mammary epithelial cells

Somatic cell hybrids between MCF-7 human breast cancer cells and normal immortalized human mammary epithelial cells have been obtained by polyethylene glycol-mediated cell fusion. The hybrid cells are suppressed in their ability to form tumors in nude mice, as well as in traits specific to the tumorigenic MCF-7 parent: growth factor independence, tumor necrosis factor sensitivity, and pS2 gene expression. In addition, they display other characteristics of the "normal" parent, including increased expression relative to the MCF-7 cells of the genes for the extracellular matrix component fibronectin, the intermediate filament keratin 5, and the angiogenesis inhibitor thrombospondin. The levels of keratins 8 and 18 also resemble those of the nontumorigenic parent. These results provide evidence for the existence of tumor suppressor gene products in immortal mammary epithelial cells. We propose a characteristic "suppressed" tumor cell phenotype, which encompasses altered cytoarchitecture, angiogenesis capabilities, and growth factor requirements.

Keratins as markers that distinguish normal and tumor-derived mammary epithelial cells

Keratin 5 (K5) mRNA and protein are shown to be expressed in normal mammary epithelial cells in culture and are absent from tumor-derived cell lines. To extend these findings, the full complements of keratins in normal, immortalized, and tumor cells were compared. It is shown here that normal cells produce keratins K5, K6, K7, K14, and K17, whereas tumor cells produce mainly keratins K8, K18, and K19. In immortalized cells, which are preneoplastic or partially transformed, the levels of K5 mRNA and protein are lower than in normal cells, whereas the amount of K18 is increased. Thus, K5 is an important marker in the tumorigenic process, distinguishing normal from tumor cells, and decreased K5 expression correlates with tumorigenic progression.

Specific cellular proteins bind to critical promoter sequences of the adenovirus early EIIa promoter

As an approach to the identification of essential factors required for specific expression of the adenovirus type 2 EIIaE early (EIIaE) promoter, an in vitro system was established. Under appropriate conditions, using crude extracts of non-infected HeLa cells, efficient and accurate EIIaE expression has been reproduced. As in vivo, this transcription was strongly dependent upon the integrity of two non-consensus TATA-like elements, T1 and T2, corresponding to the major (EIIaE1) and minor (EIIaE2) start sites, respectively, as well as upon intact upstream elements (A, between -40 and -50 and B, between -70 and -90) common to both overlapping promoters. The implication of specific DNA-binding proteins in the transcriptional effects mediated by these elements was demonstrated by DNAse I footprinting analyses. Both crude nuclear extracts and partially purified fractions confer specific protection against DNAse I digestion to the T1 and B promoter elements defined above, and to a far upstream region (element C, between -110 and -150), which has previously been identified as a weaker promoter element by in vivo transcriptional studies. Separation of the T1 recognition factor from those which bind to the upstream elements B and C by chromatographic fractionation of the extracts has also been achieved.

E1a inducibility of the adenoviral early E2a promoter is determined by specific combinations of sequence elements

By transient expression analysis in HeLa cells of adenovirus-2 E2a early (E2aE) promoter mutants and hybrid E2aE-beta-globin gene constructs, we demonstrate the existence of three nucleotide (nt) sequence elements involved in the E1a-responsiveness of the E2aE transcription unit: element I, localized within a segment (nt -13 to +62) surrounding the major E2aE cap site (nt + 1); element II (between nt -71 and -29), and element III (between nt -146 and -86). Each element is unable by itself to confer E1a responsiveness. Only combinations of sequences including elements I and II (spanning nt -71 and +62) or II and III (spanning nt -146 and -29) ensure maximal inducibility, for which element II appears of central importance.

The adenovirus-2 early EIIa transcription unit possesses two overlapping promoters with different sequence requirements for EIa-dependent stimulation

The EIa-inducible, EIIa transcription unit of adenovirus-2 is transcribed early in infection from two start sites (+1 or EIIaE1 and -26 or EIIaE2), neither of which is preceded by canonical TATA box elements. Analysis of promoter deletion and linker scanning mutations for in vivo transcriptional activity after transfection into HeLa cells has indicated the existence of two overlapping promoters in the EIIaE gene. Two regions, each approximately 30 nucleotides upstream from start sites EIIaE1 and EIIaE2, function as TATA box substitutes. A sequence centered at position -42 (with respect to the major start site at position +1) is essential for transcription from both sites, while an element further upstream, localized between nucleotides -91 and -62, is also required for efficient EIIaE transcription, with the 3' border being dispensable for EIIaE2 transcription. Analysis of the entire series of EIIaE mutants, co-transfected with an EIa-containing plasmid, revealed that no unique sequence elements in the EIIaE1 promoter region between -97 and +1 were responsible for the stimulation of EIIaE1 transcription by EIa. In contrast, the EIa-mediated augmentation of EIIaE2 template activity was mainly dependent upon a sequence, the 5'-TTAAATTT-3' putative TATA box substitute, located around position -59.