Novel recruitment approaches and operational results for a statewide population Cohort for cancer research: The Healthy Oregon Project

Background

Cancer health research relies on large-scale cohorts to derive generalizable results for different populations. While traditional epidemiological cohorts often use costly random sampling or self-motivated, preselected groups, a shift toward health system-based cohorts has emerged. However, such cohorts depend on participants remaining within a single system. Recent consumer engagement models using smartphone-based communication, driving projects, and social media have begun to upend these paradigms.

Methods

We initiated the Healthy Oregon Project (HOP) to support basic and clinical cancer research. HOP study employs a novel, cost-effective remote recruitment approach to effectively establish a large-scale cohort for population-based studies. The recruitment leverages the unique email account, the HOP website, and social media platforms to direct smartphone users to the study app, which facilitates saliva sample collection and survey administration. Monthly newsletters further facilitate engagement and outreach to broader communities.

Results

By the end of 2022, the HOP has enrolled approximately 35,000 participants aged 18-100 years (median = 44.2 years), comprising more than 1% of the Oregon adult population. Among those who have app access, ∼87% provided consent to genetic screening. The HOP monthly email newsletters have an average open rate of 38%. Efforts continue to be made to improve survey response rates.

Conclusion

This study underscores the efficacy of remote recruitment approaches in establishing large-scale cohorts for population-based cancer studies. The implementation of the study facilitates the collection of extensive survey and biological data into a repository that can be broadly shared and supports collaborative clinical and translational research.

Population screening shows risk of inherited cancer and familial hypercholesterolemia in Oregon

The Healthy Oregon Project (HOP) is a statewide effort that aims to build a large research repository and influence the health of Oregonians through providing no-cost genetic screening to participants for a next-generation sequencing 32-gene panel comprising genes related to inherited cancers and familial hypercholesterolemia. This type of unbiased population screening can detect at-risk individuals who may otherwise be missed by conventional medical approaches. However, challenges exist for this type of high-throughput testing in an academic setting, including developing a low-cost high-efficiency test and scaling up the clinical laboratory for processing large numbers of samples. Modifications to our academic clinical laboratory including efficient test design, robotics, and a streamlined analysis approach increased our ability to test more than 1,000 samples per month for HOP using only one dedicated HOP laboratory technologist. Additionally, enrollment using a HIPAA-compliant smartphone app and sample collection using mouthwash increased efficiency and reduced cost. Here, we present our experience three years into HOP and discuss the lessons learned, including our successes, challenges, opportunities, and future directions, as well as the genetic screening results for the first 13,670 participants tested. Overall, we have identified 730 pathogenic/likely pathogenic variants in 710 participants in 24 of the 32 genes on the panel. The carrier rate for pathogenic/likely pathogenic variants in the inherited cancer genes on the panel for an unselected population was 5.0% and for familial hypercholesterolemia was 0.3%. Our laboratory experience described here may provide a useful model for population screening projects in other states.

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin, and drivers of ITH across cancer types are poorly understood. To address this, we extensively characterize ITH across whole-genome sequences of 2,658 cancer samples spanning 38 cancer types. Nearly all informative samples (95.1%) contain evidence of distinct subclonal expansions with frequent branching relationships between subclones. We observe positive selection of subclonal driver mutations across most cancer types and identify cancer type-specific subclonal patterns of driver gene mutations, fusions, structural variants, and copy number alterations as well as dynamic changes in mutational processes between subclonal expansions. Our results underline the importance of ITH and its drivers in tumor evolution and provide a pan-cancer resource of comprehensively annotated subclonal events from whole-genome sequencing data.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

The evolutionary history of 2,658 cancers

Cancer develops through a process of somatic evolution1,2. Sequencing data from a single biopsy represent a snapshot of this process that can reveal the timing of specific genomic aberrations and the changing influence of mutational processes3. Here, by whole-genome sequencing analysis of 2,658 cancers as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)4, we reconstruct the life history and evolution of mutational processes and driver mutation sequences of 38 types of cancer. Early oncogenesis is characterized by mutations in a constrained set of driver genes, and specific copy number gains, such as trisomy 7 in glioblastoma and isochromosome 17q in medulloblastoma. The mutational spectrum changes significantly throughout tumour evolution in 40% of samples. A nearly fourfold diversification of driver genes and increased genomic instability are features of later stages. Copy number alterations often occur in mitotic crises, and lead to simultaneous gains of chromosomal segments. Timing analyses suggest that driver mutations often precede diagnosis by many years, if not decades. Together, these results determine the evolutionary trajectories of cancer, and highlight opportunities for early cancer detection.

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the ΔNp63 oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support possibilities for molecular classification and therapeutic approaches.

Abstract 2286: Liquid biopsy for early cancer detection

Introduction: Early cancer detection remains as a critical challenge to improve patient’s survival and clinical outcome. A non-invasive liquid biopsy permits the analysis of multiple circulating biomarkers including cell free nucleic acids and extracellular vesicles that facilitate the discovery of disease. We hypothesize that cancer-derived circulating biomarkers contain heterogeneous surface membrane proteins and/or nucleic acids representing the original tumor, requiring tools which can identify multiple biomarkers to be detected simultaneously. However, challenges including a lack of established isolation standards and determining sufficiently sensitive detection platforms remain for clinical implementation. Our goal is to develop a multiplexed biomarker based assay which can be leveraged to capture the molecular heterogeneity of distinct subpopulations of tumor derived circulating biomarkers.

Materials and Methods: Materials and methods vary greatly by project, each project design will be briefly summarized: 1) Single molecule imaging of ctDNA was conducted using PEG-coated surface whereby biotin streptavidin linked DNA reference strands were exposed to fluorophore conjugated mutant DNA strands for FRET imaging of mutant specific sequences. 2) Extracellular vesicle imaging and profiling was conducted using antibody based surface capture and high-resolution flow cytometry for high throughput exosome characterization. 3) RNA-biomarkers were identified by converting RNA into cDNA using target gene panels selected from data bases at each cycle during a PCR.

Results and Discussion: RNA profiling of initial sample cohort distinguished cancer from healthy, while detecting early cancer patients with high sensitivity. Differentiating genes with biological relevance were identified which can classify pancreatic cancer patients from healthy donor. cfDNA imaging method had nonspecific signal < 0.1-1%, wherein 1-10% mutant fraction can be genotyped. High resolution flow cytometry identified distinct subpopulations of plasma exosomes and revealed their molecular heterogeneity and cancer specific marker candidates can be screened against purified exosomes.

Conclusions: Extracellular vesicle imaging and profiling co-validated by high resolution flow cytometry, exemplifying the utility of a multi-platform detection scheme to characterize plasma-derived extracellular vesicle populations. Cell free RNA biomarkers of cancer by cell-free RNA sequencing were analyzed that can improve early cancer detection outcome, this proof of concept was done on pancreatic patient plasma and is being expanded into other cancer cohorts.

Citation Format: Hyunji Kim, Fehmi Civitci, Josiah Wagner, Pavana Anur, Matthew Rames, Xiaolin Nan, Terry Morgan, Thuy Ngo. Liquid biopsy for early cancer detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2286.

Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets

The roles of tumor-associated macrophages (TAMs) and circulating monocytes in human cancer are poorly understood. Here, we show that monocyte subpopulation distribution and transcriptomes are significantly altered by the presence of endometrial and breast cancer. Furthermore, TAMs from endometrial and breast cancers are transcriptionally distinct from monocytes and their respective tissue-resident macrophages. We identified a breast TAM signature that is highly enriched in aggressive breast cancer subtypes and associated with shorter disease-specific survival. We also identified an auto-regulatory loop between TAMs and cancer cells driven by tumor necrosis factor alpha involving SIGLEC1 and CCL8, which is self-reinforcing through the production of CSF1. Together these data provide direct evidence that monocyte and macrophage transcriptional landscapes are perturbed by cancer, reflecting patient outcomes.

Abstract 218: The evolutionary history of 2,658 cancers

Cancer develops through a continuous process of somatic evolution. Whole genome sequencing provides a snapshot of the tumor genome at the point of sampling, however, the data can contain information that permits the reconstruction of a tumor's evolutionary past.

Here, we apply such life history analyses on an unprecedented scale, to a set of 2,658 tumors spanning 39 cancer types. We estimated the timing of large chromosomal gains during tumor evolution, by comparing the rates of doubled to non-doubled point mutations within gained regions. Although we find that such events typically occur in the second half of clonal evolution, we also observe distinctive and early chromosomal gains in some cancer types, such as gains of chromosomes 7, 19 and 20 in glioblastoma, and isochromosome 17q in medulloblastoma. By integrating these results with the qualitative timing of individual driver mutations, we obtained an overall ranking, from early to late, of frequent somatic events per cancer type, which both identified novel patterns of tumor evolution, and incorporated additional detail into known models, such as the progression of APC-KRAS-TP53 in colorectal cancer proposed by Vogelstein and Fearon.

To estimate how mutational processes acting on the tumor genome change over time, we classified mutations in each sample according to three broad time periods (early clonal, late clonal, and subclonal), and quantified the activity of mutational signatures in each period. Most mutational processes appear to remain remarkably constant, however, certain signatures show clear and consistent changes during clonal evolution. Particularly, mutational signatures associated with exposure to carcinogens, such as smoking and UV light, tend to decrease over time. In contrast, signatures associated with defective endogenous processes, such as APOBEC mutagenesis and defective double strand break repair, show an increase between early and late phases of tumor evolution.

Making use of clock-like mutational signatures, we converted mutational time estimates for large events, such as whole genome duplication (WGD), and the emergence of the most recent common ancestor (MRCA), into real time estimates, which allowed us to combine our analyses into overall timelines of cancer evolution, per tumor type. For example, the typical timeline of ovarian adenocarcinoma development shows that early tumor evolution is characterized by mutations in TP53, and widespread genome instability, with WGD events taking place on average 8 years prior to diagnosis. In later stages of evolution, signatures of defective repair processes increase, and the MRCA emerges on average 1 year before diagnosis.

Taken together, these data reveal the common and divergent evolutionary trajectories available to a cancer, which might be crucial in understanding specific tumor biology, and in providing new opportunities for early detection and cancer prevention.

Citation Format: Clemency Jolly, Moritz Gerstung, Ignaty Leshchiner, Stefan C. Dentro, Santiago Gonzalez, Thomas J. Mitchell, Yulia Rubanova, Pavana Anur, Daniel Rosebrock, Kaixian Yu, Maxime Tarabichi, Amit Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vásquez-García, Kerstin Haase, Subhajit Sengupta, Geoff Macintyre, Salem Malikic, Nilgun Donmez, Dimitri G. Livitz, Mark Cmero, Jonas Demeulemeester, Steve Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C. Boutros, David D. Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, S Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Juan, Wenyi Wang, Quaid D. Morris, Paul T. Spellman, David C. Wedge, Peter Van Loo, PCAWG Evolution and Heterogeneity Working Group. The evolutionary history of 2,658 cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 218.

Molecular Cytogenetics Guides Massively Parallel Sequencing of a Radiation-Induced Chromosome Translocation in Human Cells

Chromosome rearrangements are large-scale structural variants that are recognized drivers of oncogenic events in cancers of all types. Cytogenetics allows for their rapid, genome-wide detection, but does not provide gene-level resolution. Massively parallel sequencing (MPS) promises DNA sequence-level characterization of the specific breakpoints involved, but is strongly influenced by bioinformatics filters that affect detection efficiency. We sought to characterize the breakpoint junctions of chromosomal translocations and inversions in the clonal derivatives of human cells exposed to ionizing radiation. Here, we describe the first successful use of DNA paired-end analysis to locate and sequence across the breakpoint junctions of a radiation-induced reciprocal translocation. The analyses employed, with varying degrees of success, several well-known bioinformatics algorithms, a task made difficult by the involvement of repetitive DNA sequences. As for underlying mechanisms, the results of Sanger sequencing suggested that the translocation in question was likely formed via microhomology-mediated non-homologous end joining (mmNHEJ). To our knowledge, this represents the first use of MPS to characterize the breakpoint junctions of a radiation-induced chromosomal translocation in human cells. Curiously, these same approaches were unsuccessful when applied to the analysis of inversions previously identified by directional genomic hybridization (dGH). We conclude that molecular cytogenetics continues to provide critical guidance for structural variant discovery, validation and in "tuning" analysis filters to enable robust breakpoint identification at the base pair level.

The Integrated Genomic Landscape of Thymic Epithelial Tumors

Thymic epithelial tumors (TETs) are one of the rarest adult malignancies. Among TETs, thymoma is the most predominant, characterized by a unique association with autoimmune diseases, followed by thymic carcinoma, which is less common but more clinically aggressive. Using multi-platform omics analyses on 117 TETs, we define four subtypes of these tumors defined by genomic hallmarks and an association with survival and World Health Organization histological subtype. We further demonstrate a marked prevalence of a thymoma-specific mutated oncogene, GTF2I, and explore its biological effects on multi-platform analysis. We further observe enrichment of mutations in HRAS, NRAS, and TP53. Last, we identify a molecular link between thymoma and the autoimmune disease myasthenia gravis, characterized by tumoral overexpression of muscle autoantigens, and increased aneuploidy.

MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection

To build a catalog of peptides presented by breast cancer cells, we undertook systematic MHC class I immunoprecipitation followed by elution of MHC class I-loaded peptides in breast cancer cells. We determined the sequence of 3196 MHC class I ligands representing 1921 proteins from a panel of 20 breast cancer cell lines. After removing duplicate peptides, i.e., the same peptide eluted from more than one cell line, the total number of unique peptides was 2740. Of the unique peptides eluted, more than 1750 had been previously identified, and of these, sixteen have been shown to be immunogenic. Importantly, half of these immunogenic peptides were shared between different breast cancer cell lines. MHC class I binding probability was used to plot the distribution of the eluted peptides in accordance with the binding score for each breast cancer cell line. We also determined that the tested breast cancer cells presented 89 mutation-containing peptides and peptides derived from aberrantly translated genes, 7 of which were shared between four or two different cell lines. Overall, the high throughput identification of MHC class I-loaded peptides is an effective strategy for systematic characterization of cancer peptides, and could be employed for design of multi-peptide anticancer vaccines.

SIGNIFICANCE

By employing proteomic analyses of eluted peptides from breast cancer cells, the current study has built an initial HLA-I-typed antigen collection for breast cancer research. It was also determined that immunogenic epitopes can be identified using established cell lines and that shared immunogenic peptides can be found in different cancer types such as breast cancer and leukemia. Importantly, out of 3196 eluted peptides that included duplicate peptides in different cells 89 peptides either contained mutation in their sequence or were derived from aberrant translation suggesting that mutation-containing epitopes are on the order of 2-3% in breast cancer cells. Finally, our results suggest that interfering with MHC class I function is one of the mechanisms of how tumor cells escape immune system attack.

ΔN-ASPP2, a novel isoform of the ASPP2 tumor suppressor, promotes cellular survival

ASPP2 is a tumor suppressor that works, at least in part, through enhancing p53-dependent apoptosis. We now describe a new ASPP2 isoform, ΔN-ASPP2, generated from an internal transcription start site that encodes an N-terminally truncated protein missing a predicted 254 amino acids. ΔN-ASPP2 suppresses p53 target gene transactivation, promoter occupancy, and endogenous p53 target gene expression in response to DNA damage. Moreover, ΔN-ASPP2 promotes progression through the cell cycle, as well as resistance to genotoxic stress-induced growth inhibition and apoptosis. Additionally, we found that ΔN-ASPP2 expression is increased in human breast tumors as compared to adjacent normal breast tissue; in contrast, ASPP2 is suppressed in the majority of these breast tumors. Together, our results provide insight into how this new ASPP2 isoform may play a role in regulating the ASPP2-p53 axis.

Late effects in patients with Fanconi anemia following allogeneic hematopoietic stem cell transplantation from alternative donors

Hematopoietic stem cell transplantation (HSCT) is curative for hematological manifestations of Fanconi anemia (FA). We performed a retrospective analysis of 22 patients with FA and aplastic anemia, myelodysplastic syndrome or acute myelogenous leukemia who underwent a HSCT at Memorial Sloan Kettering Cancer Center and survived at least 1 year post HSCT. Patients underwent either a TBI- (N=18) or busulfan- (N=4) based cytoreduction followed by T-cell-depleted transplants from alternative donors. Twenty patients were alive at time of the study with a 5- and 10-year overall survival of 100 and 84% and no evidence of chronic GvHD. Among the 18 patients receiving a TBI-based regimen, 11 (61%) had persistent hemochromatosis, 4 (22%) developed hypothyroidism, 7 (39%) had insulin resistance and 5 (27%) developed hypertriglyceridemia after transplant. Eleven of 16 evaluable patients (68%), receiving TBI, developed gonadal dysfunction. Two patients who received a TBI-based regimen died of squamous cell carcinoma. One patient developed hemochromatosis, hypothyroidism and gonadal dysfunction after busulfan-based cytoreduction. TBI appears to be a risk factor for malignant and endocrine late effects in the FA host. Multidisciplinary follow-up of patients with FA (including cancer screening) is essential for early detection and management of late complications, and improving long-term outcomes.

Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma

BACKGROUND

Papillary renal-cell carcinoma, which accounts for 15 to 20% of renal-cell carcinomas, is a heterogeneous disease that consists of various types of renal cancer, including tumors with indolent, multifocal presentation and solitary tumors with an aggressive, highly lethal phenotype. Little is known about the genetic basis of sporadic papillary renal-cell carcinoma, and no effective forms of therapy for advanced disease exist.

METHODS

We performed comprehensive molecular characterization of 161 primary papillary renal-cell carcinomas, using whole-exome sequencing, copy-number analysis, messenger RNA and microRNA sequencing, DNA-methylation analysis, and proteomic analysis.

RESULTS

Type 1 and type 2 papillary renal-cell carcinomas were shown to be different types of renal cancer characterized by specific genetic alterations, with type 2 further classified into three individual subgroups on the basis of molecular differences associated with patient survival. Type 1 tumors were associated with MET alterations, whereas type 2 tumors were characterized by CDKN2A silencing, SETD2 mutations, TFE3 fusions, and increased expression of the NRF2-antioxidant response element (ARE) pathway. A CpG island methylator phenotype (CIMP) was observed in a distinct subgroup of type 2 papillary renal-cell carcinomas that was characterized by poor survival and mutation of the gene encoding fumarate hydratase (FH).

CONCLUSIONS

Type 1 and type 2 papillary renal-cell carcinomas were shown to be clinically and biologically distinct. Alterations in the MET pathway were associated with type 1, and activation of the NRF2-ARE pathway was associated with type 2; CDKN2A loss and CIMP in type 2 conveyed a poor prognosis. Furthermore, type 2 papillary renal-cell carcinoma consisted of at least three subtypes based on molecular and phenotypic features. (Funded by the National Institutes of Health.).

Abstract PD6-2: FoxA1 gene amplification in ER+ breast cancer mediates endocrine resistance by increasing IL-8

Background: ER transcriptional programming is associated with fundamental changes when endocrine resistance develops. The Forkhead transcription factor, FoxA1, is a pioneer factor for ER-DNA binding. We hypothesize that FoxA1 plays a critical role in ER transcriptional reprogramming in endocrine resistance by augmenting itself and the specific downstream effectors. Methods: Next generation sequencing was applied to characterize a panel of endocrine-resistant (Endo-R) cell models. Genomic PCR amplification and FISH assays were developed to measure FoxA1 copy number gain (CNG). Q-RT-PCR, Western blots, IHC, ELISA, and cytokine arrays were used to determine the levels of FoxA1 and IL-8 in cell culture and in vivo xenograft tumors. Effects of gene knockdown (ER, FoxA1, or IL-8) or inducible FoxA1 overexpression on ER and growth factor receptor (GFR) downstream signaling were determined by cell growth and Western blots. ER and FoxA1 binding at the IL-8 gene locus was measured by ChIP-qPCR. ChIP-seq analysis was integrated with RNA-seq data. Kaplan-Meier analysis evaluated the predictive role of FoxA1in ER+ breast tumors. Results: Exome-seq revealed that FoxA1 is the most highly amplified gene in TamR vs. P cells from two independent MCF7 models. Genomic PCR and FISH also indicate FoxA1 CNG in Endo-R models of ZR75-1 and BT474. Increased FoxA1 expression was found in multiple Endo-R cells and in MCF7L Endo-R xenograft tumors. Cytokines, especially IL-8, are more highly expressed in multiple Endo-R cell models, similar to our previous microarray data from MCF7 Endo-R xenograft tumors. FoxA1 forced overexpression significantly induced IL-8 expression in MCF7L-P cells. It also activated multiple GFR downstream signaling pathways, and conferred endocrine resistance. Conversely, knockdown of either FoxA1 or ER significantly decreased IL-8 levels in TamR cells, and inhibited cell growth in both P and TamR cells. Knockdown of IL-8 in TamR cells substantially inhibited GFR downstream signaling, and was more cytotoxic than in P cells. A novel FoxA1-binding site (10 kb at 5’UTR of IL-8) recruited more FoxA1 and p300 in MCF7L-TamR than -P cells. ChIP-seq shows a general enhancement of FoxA1 binding around the genes (within 20 kb) that are differentially expressed in TamR vs. P cells. We identified a FoxA1 CNG-associated gene signature from TCGA breast tumors that predicts worse relapse-free survival (RFS) in Tam-treated ER+ tumors (from Loi et al). Meta-analysis showed that FoxA1 mRNA levels in the top 25th percentile predict worse RFS in ER+ patients treated with Tam (N=615), but not in systemically untreated patients (N=500). FoxA1 CNG and overexpression in clinical specimens by using our newly developed FISH and IHC assays are currently being investigated. Conclusions: FoxA1 gene amplification was enriched in two independent MCF7 Tam-R cell models. Clonal selection of FoxA1 gene amplification may occur and lead to endocrine resistance. High levels of FoxA1 may mediate endocrine resistance by directly inducing IL-8. The data suggest that IL-8 signaling is a component of a cytokine loop controlled by the FoxA1/ER transcriptional reprogramming, which might be exploited in therapeutics to overcome endocrine resistance.

Citation Format: Xiaoyong Fu, Rinath Jeselsohn, Emporia F Hollingsworth, Dolores Lopez-Terrada, Chad J Creighton, Agostina Nardone, Martin Shea, Laura M Heiser, Pavana Anur, Nicholas Wang, Catie Grasso, Paul Spellman, Carolina Gutierrez, Mothaffar F Rimawi, Susan G Hilsenbeck, Joe W Gray, Myles Brown, C K Osborne, Rachel Schiff. FoxA1 gene amplification in ER+ breast cancer mediates endocrine resistance by increasing IL-8 [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr PD6-2.

Overcoming endocrine resistance due to reduced PTEN levels in estrogen receptor-positive breast cancer by co-targeting mammalian target of rapamycin, protein kinase B, or mitogen-activated protein kinase kinase

INTRODUCTION

Activation of the phosphatidylinositol 3-kinase (PI3K) pathway in estrogen receptor α (ER)-positive breast cancer is associated with reduced ER expression and activity, luminal B subtype, and poor outcome. Phosphatase and tensin homolog (PTEN), a negative regulator of this pathway, is typically lost in ER-negative breast cancer. We set out to clarify the role of reduced PTEN levels in endocrine resistance, and to explore the combination of newly developed PI3K downstream kinase inhibitors to overcome this resistance.

METHODS

Altered cellular signaling, gene expression, and endocrine sensitivity were determined in inducible PTEN-knockdown ER-positive/human epidermal growth factor receptor 2 (HER2)-negative breast cancer cell and/or xenograft models. Single or two-agent combinations of kinase inhibitors were examined to improve endocrine therapy.

RESULTS

Moderate PTEN reduction was sufficient to enhance PI3K signaling, generate a gene signature associated with the luminal B subtype of breast cancer, and cause endocrine resistance in vitro and in vivo. The mammalian target of rapamycin (mTOR), protein kinase B (AKT), or mitogen-activated protein kinase kinase (MEK) inhibitors, alone or in combination, improved endocrine therapy, but the efficacy varied by PTEN levels, type of endocrine therapy, and the specific inhibitor(s). A single-agent AKT inhibitor combined with fulvestrant conferred superior efficacy in overcoming resistance, inducing apoptosis and tumor regression.

CONCLUSIONS

Moderate reduction in PTEN, without complete loss, can activate the PI3K pathway to cause endocrine resistance in ER-positive breast cancer, which can be overcome by combining endocrine therapy with inhibitors of the PI3K pathway. Our data suggests that the ER degrader fulvestrant, to block both ligand-dependent and -independent ER signaling, combined with an AKT inhibitor is an effective strategy to test in patients.

c-Src modulates estrogen-induced stress and apoptosis in estrogen-deprived breast cancer cells

The emergence of anti-estrogen resistance in breast cancer is an important clinical phenomenon affecting long-term survival in this disease. Identifying factors that convey cell survival in this setting may guide improvements in treatment. Estrogen (E2) can induce apoptosis in breast cancer cells that have been selected for survival after E2 deprivation for long periods (MCF-7:5C cells), but the mechanisms underlying E2-induced stress in this setting have not been elucidated. Here, we report that the c-Src kinase functions as a key adapter protein for the estrogen receptor (ER, ESR1) in its activation of stress responses induced by E2 in MCF-7:5C cells. E2 elevated phosphorylation of c-Src, which was blocked by 4-hydroxytamoxifen (4-OHT), suggesting that E2 activated c-Src through the ER. We found that E2 activated the sensors of the unfolded protein response (UPR), IRE1α (ERN1) and PERK kinase (EIF2AK3), the latter of which phosphorylates eukaryotic translation initiation factor-2α (eIF2α). E2 also dramatically increased reactive oxygen species production and upregulated expression of heme oxygenase HO-1 (HMOX1), an indicator of oxidative stress, along with the central energy sensor kinase AMPK (PRKAA2). Pharmacologic or RNA interference-mediated inhibition of c-Src abolished the phosphorylation of eIF2α and AMPK, blocked E2-induced ROS production, and inhibited E2-induced apoptosis. Together, our results establish that c-Src kinase mediates stresses generated by E2 in long-term E2-deprived cells that trigger apoptosis. This work offers a mechanistic rationale for a new approach in the treatment of endocrine-resistant breast cancer.

Identification and characterization of T cell epitopes expressed on the surface of cancer cells. (P2002)

In our search for better ways to stimulate anti-tumor T cell-mediated immune response we optimized powerful technique known as “reverse” immunogenetics, in which MHC I-bound peptides are recovered and sequenced using highly sensitive mass spectrometry. Using this technique we have identified more than 3,500 peptides eluted from the surface of 20 breast carcinoma cell lines of 4 different subtypes. By using sequence data for each breast carcinoma cell line we predicted bound peptide consensus sequence for a particular allele of HLA-A, -B, and C molecules. Next, we determined the frequency of the identification of both peptide and protein that is associated with this peptide in subtype-specific and all analyzed cell lines. This allowed us to associate some MHC I-presented peptides/proteins with a specific subtype of breast cancer as well as shared peptides/proteins. Some of the identified proteins are tumor specific and immunogenic. For example, Aldolase A, which is MHC I-presented in many cell lines, has been identified by Serex analysis in lung cancer and breast cancer patients. Lastly, using gene expression data for 60 breast carcinoma and normal cell lines as well as for 708 tumors and 329 normal tissues we have sorted all identified proteins in accordance with the level of their expression in non-transformed and transformed cells. This arrangement allowed us to identify, for the first time, several tumor specific genes that could be good targets for T cell-based therapy.

Phospholipid Scramblase 1, an interferon-regulated gene located at 3q23, is regulated by SnoN/SkiL in ovarian cancer cells

Background

Treatment of advanced stage ovarian cancer continues to be challenging due to acquired drug resistance and lack of early stage biomarkers. Genes identified to be aberrantly expressed at the 3q26.2 locus (i.e. SnoN/SkiL) have been implicated in ovarian cancer pathophysiology. We have previously shown that SnoN expression is increased in advanced stage ovarian cancers and alters cellular response to arsenic trioxide (As₂O₃).

Findings

We now demonstrate increased DNA copy number levels (TCGA data) of phospholipid scramblase 1 (PLSCR1, located at 3q23) whose transcript expression in ovarian cell lines is highly correlated with SnoN mRNA. Interestingly, SnoN can modulate PLSCR1 mRNA levels in the absence/presence of interferon (IFN-2α). Both IFN-2α and As₂O₃ treatment can modulate PLSCR1 mRNA levels in ovarian carcinoma cells. However, SnoN siRNA does not lead to altered PLSCR1 protein implicating other events needed to modulate its protein levels. In addition, we report that PLSCR1 can modulate aspects of the As₂O₃ cellular response.

Conclusions

Our findings warrant further investigation into the role of PLSCR1 in ovarian cancer development and chemoresistance.

Abstract 5238: Acquired therapeutic resistance is mediated by deregulation of multiple pathways

The HER2-directed antibody, trastuzumab combined with chemotherapy, has markedly improved outcome of patients with HER2-amplified breast cancer, yet both de novo and acquired resistance occur in a substantial subset of patients. To study the molecular underpinnings of acquired resistance, we have developed a panel of 30 unique HER2+ cell lines that have been cultured to become resistant to lapatinib, trastuzumab and the combination treatment. Each of these models underwent next-generation sequencing to elucidate mechanisms of resistance to HER2 therapies. We hypothesized that resistance may be mediated by modulation of particular pathways - rather than by individual genes. With this idea in mind, we performed a PARADIGM pathway analysis that integrates information from multiple genomic data types to calculate pathway activity scores. The PARADIGM SuperPathways represent 1321 cell signaling pathways curated from sources such as KEGG, BioCarta, and Reactome. We populated the networks with the copy number (ExomeSeq) and expression (RNAseq) datasets that had been normalized to identify contrasts between parental and resistant lines. For each pathway, we computed a Pathway Activity Score as the sum of the absolute value of each node in the pathway, normalized by the total number of pathway nodes. Nearly 30% of the curated pathways (361/1321) are strongly deregulated in at least one of the network models, whereas a much smaller subset (3%) were strongly deregulated across multiple resistance cell line models. Frequently deregulated pathways include hemoglobin chaperone, ATM mediated phosphorylation of repair proteins, the HIF2alpha transcription factor network and the PLK signaling events in the cell cycle. All together, these findings indicate that resistance is mediated through many signaling mechanisms. Furthermore, the acquired resistance-related aberrations suggest possible second-line treatment strategies that may be effective.

Citation Format: Laura M. Heiser, Chad A. Shaw, Nicholas J. Wang, Catie Grasso, Pavana Anur, Sam Ng, Theodore Goldstein, Paul T. Spellman, Joshua Stuart, Kent Osborne, Joe Gray, Rachel Schiff. Acquired therapeutic resistance is mediated by deregulation of multiple pathways. [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 5238. doi:10.1158/1538-7445.AM2013-5238

Abstract 2921: Critical mediation of E2-induced apoptosis through c-Src in long-term estrogen deprived breast cancer cells

Our previous publication showed that physiological concentrations of estrogen (E2) could trigger apoptosis of long-term E2 deprived breast cancer cells (MCF-7:5C) (Lewis et al. JNCI 2005; 97:1746-59). This new targeted strategy provides novel therapeutic approaches to endocrine resistant breast cancer. A phase II clinical trial reported that E2 provided a clinical benefit for aromatase inhibitor-resistant advanced breast cancer patients. However, only 30% of patients receive clinical benefit (Ellis MJ et al. JAMA 2009;302:774-80). This prompted us to investigate the mechanisms underlying E2-induced apoptosis to find strategies to increase the therapeutic responsiveness. c-Src is currently of interest, as it is an important adapter protein of ER in breast cancer cells. Here, we found that E2 stimulated c-Src phosphorylation in MCF-7:5C cells and 4-hydroxytamoxifen (4-OHT) could block this stimulation which demonstrated that E2 activated c-Src through ER. The specific inhibitor of c-Src, PP2, could block c-Src activation induced by E2. E2 rapidly activated growth pathways within minutes in MCF-7:5C cells and PP2 could block this non-genomic pathway. E2 was also able to activate Akt/MAPK pathways after 24 hour treatment which could be blocked by inhibition of c-Src. These data showed that c-Src mediated downstream signaling pathways of ER in MCF-7:5C cells. Characteristic E2-induced apoptosis occurred around 72 hour treatment with E2, unexpectedly, inhibition of c-Src could significantly block E2-induced apoptosis which implied that c-Src played a critical role in E2-induced apoptosis. Further examination through transcriptome analysis confirmed that E2 widely induced apoptosis-related pathways. Consistent with the biological experiments, PP2 could completely abolish the apoptosis pathways induced by E2. These data illustrate that c-Src acts as a critical molecule to mediate the downstream signaling of ER (including E2-induced apoptosis) in MCF-7:5C cells. It provides an important rationale for clinical trial with c-Src inhibitors in aromatase inhibitors resistant patients, especially avoiding in combination with physiological levels of E2. Acknowledgements This work (VCJ and JWG) is supported by the SU2C (AACR) Grant (SU2C-AACR-DT0409).

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 2921. doi:1538-7445.AM2012-2921