Initial Phase I Safety Study of Gedatolisib plus Cofetuzumab Pelidotin for Patients with Metastatic Triple-Negative Breast Cancer

PURPOSE

The PI3K pathway is dysregulated in the majority of triple-negative breast cancers (TNBC), yet single-agent inhibition of PI3K has been ineffective in TNBC. PI3K inhibition leads to an immediate compensatory upregulation of the Wnt pathway. Dual targeting of both pathways is highly synergistic against TNBC models in vitro and in vivo. We initiated a phase I clinical trial combining gedatolisib, a pan-class I isoform PI3K/mTOR inhibitor, and cofetuzumab pelidotin, an antibody-drug conjugate against the cell-surface PTK7 protein (Wnt pathway coreceptor) with an auristatin payload.

PATIENTS AND METHODS

Participants (pt) had metastatic TNBC or estrogen receptor (ER) low (ER and PgR < 5%, HER2-negative) breast cancer, and had received at least one prior chemotherapy for advanced disease. The primary objective was safety. Secondary endpoints included overall response rate (ORR), clinical benefit at 18 weeks (CB18), progression-free survival (PFS), and correlative analyses.

RESULTS

A total of 18 pts were enrolled in three dose cohorts: gedatolisib 110 mg weekly + cofetuzumab pelidotin 1.4 mg/kg every 3 weeks (n = 4), 180 mg + 1.4 mg/kg (n = 3), and 180 mg + 2.8 mg/kg (n = 11). Nausea, anorexia, fatigue, and mucositis were common but rarely reached ≥grade 3 severity. Myelosuppression was uncommon. ORR was 16.7% (3/18). An additional 3 pts had stable disease (of these 2 had stable disease for >18 weeks); CB18 was 27.8%. Median PFS was 2.0 months (95% confidence interval for PFS: 1.2-6.2). Pts with clinical benefit were enriched with genomic alterations in the PI3K and PTK7 pathways.

CONCLUSIONS

The combination of gedatolisib + cofetuzumab pelidotin was well tolerated and demonstrated promising clinical activity. Further investigation of this drug combination in metastatic TNBC is warranted.

FAM83A is a potential biomarker for breast cancer initiation

Background

Family with sequence similarity 83 member A (FAM83A) presents oncogenic properties in several cancers including breast cancer. Recently, we reported FAM83A overexpression in normal breast tissues from women at high risk of breast cancer. We now hypothesize that FAM83A is a key factor in breast cancer initiation.

Methods

Immunohistochemical staining was used to evaluate FAM83A protein levels in both a normal breast tissue microarray (TMA, N = 411) and a breast tumor TMA (N = 349). EGFR staining and its correlation with FAM83A expression were also assessed. Lentivirus-mediated manipulation of FAM83A expression in primary and hTERT-immortalized breast epithelial cells was employed. Biological and molecular alterations upon FAM83A overexpression/downregulation and FAM83A’s interaction partners were investigated.

Results

TMA analysis revealed a 1.5-fold increase in FAM83A expression level in breast cancer cases as compared with normal breast tissues (p < 0.0001). FAM83A protein expression was directly correlated with EGFR level in both normal and breast cancer tissues. In in vitro assays, exogenous expression of FAM83A in either primary or immortalized breast epithelial cells promoted cell viability and proliferation. Additionally, Ingenuity Pathway Analysis (IPA) revealed that FAM83A overexpression in primary cells affected the expression of genes involved in cellular morphology and metabolism. Mass spectrometry analysis identified DDX3X and LAMB3 as potential FAM83A interaction partners in primary cells, while we detected FAM83A interaction with cytoskeleton reorganization factors, including LIMA1, MYH10, PLEC, MYL6 in the immortalized cells.

Conclusions

This study shows that FAM83A promotes metabolic activation in primary breast epithelial cells and cell proliferation in both primary and immortalized cells. These findings support its role in early breast oncogenesis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40364-022-00353-9.

Aberrant epigenetic and transcriptional events associated with breast cancer risk

BACKGROUND

Genome-wide association studies have identified several breast cancer susceptibility loci. However, biomarkers for risk assessment are still missing. Here, we investigated cancer-related molecular changes detected in tissues from women at high risk for breast cancer prior to disease manifestation. Disease-free breast tissue cores donated by healthy women (N = 146, median age = 39 years) were processed for both methylome (MethylCap) and transcriptome (Illumina's HiSeq4000) sequencing. Analysis of tissue microarray and primary breast epithelial cells was used to confirm gene expression dysregulation.

RESULTS

Transcriptomic analysis identified 69 differentially expressed genes between women at high and those at average risk of breast cancer (Tyrer-Cuzick model) at FDR < 0.05 and fold change ≥ 2. Majority of the identified genes were involved in DNA damage checkpoint, cell cycle, and cell adhesion. Two genes, FAM83A and NEK2, were overexpressed in tissue sections (FDR < 0.01) and primary epithelial cells (p < 0.05) from high-risk breasts. Moreover, 1698 DNA methylation changes were identified in high-risk breast tissues (FDR < 0.05), partially overlapped with cancer-related signatures, and correlated with transcriptional changes (p < 0.05, r ≤ 0.5). Finally, among the participants, 35 women donated breast biopsies at two time points, and age-related molecular alterations enhanced in high-risk subjects were identified.

CONCLUSIONS

Normal breast tissue from women at high risk of breast cancer bears molecular aberrations that may contribute to breast cancer susceptibility. This study is the first molecular characterization of the true normal breast tissues, and provides an opportunity to investigate molecular markers of breast cancer risk, which may lead to new preventive approaches.

BRE12-158: A Postneoadjuvant, Randomized Phase II Trial of Personalized Therapy Versus Treatment of Physician's Choice for Patients With Residual Triple-Negative Breast Cancer

PURPOSE

Patients with triple-negative breast cancer (TNBC) with residual disease after neoadjuvant chemotherapy (NAC) have high risk of recurrence with prior data suggesting improved outcomes with capecitabine. Targeted agents have demonstrated activity across multiple cancer types. BRE12-158 was a phase II, multicenter trial that randomly allocated patients with TNBC with residual disease after NAC to genomically directed therapy versus treatment of physician choice (TPC).

PATIENTS AND METHODS

From March 2014 to December 2018, 193 patients were enrolled. Residual tumors were sequenced using a next-generation sequencing test. A molecular tumor board adjudicated all results. Patients were randomly allocated to four cycles of genomically directed therapy (arm A) versus TPC (arm B). Patients without a target were assigned to arm B. Primary end point was 2-year disease-free survival (DFS) among randomly assigned patients. Secondary/exploratory end points included distant disease-free survival, overall survival, toxicity assessment, time-based evolution of therapy, and drug-specific outcomes.

RESULTS

One hundred ninety-three patients were randomly allocated or were assigned to arm B. The estimated 2-year DFS for the randomized population only was 56.6% (95% CI, 0.45 to 0.70) for arm A versus 62.4% (95% CI, 0.52 to 0.75) for arm B. No difference was seen in DFS, distant disease-free survival, or overall survival for the entire or randomized populations. There was increased uptake of capecitabine for TPC over time. Patients randomly allocated later had less distant recurrences. Circulating tumor DNA status remained a significant predictor of outcome with some patients demonstrating clearance with postneoadjuvant therapy.

CONCLUSION

Genomically directed therapy was not superior to TPC for patients with residual TNBC after NAC. Capecitabine should remain the standard of care; however, the activity of other agents in this setting provides rationale for testing optimal combinations to improve outcomes. Circulating tumor DNA should be considered a standard covariate for trials in this setting.

A Multicenter Phase II Trial of Ipilimumab and Nivolumab in Unresectable or Metastatic Metaplastic Breast Cancer: Cohort 36 of Dual Anti-CTLA-4 and Anti-PD-1 Blockade in Rare Tumors (DART, SWOG S1609)

PURPOSE

Metaplastic breast cancer (MpBC) is a rare aggressive subtype that responds poorly to cytotoxics. Median survival is approximately eight months for metastatic disease. We report results for advanced MpBC treated with ipilimumab+nivolumab, a cohort of S1609 for rare cancers (DART: NCT02834013).

METHODS

Prospective, open-label, multicenter phase II (two-stage) trial of ipilimumab (1mg/kg IV q6weeks) plus nivolumab (240mg IV q2weeks) for advanced MpBC. Primary endpoint was objective response rate (ORR). Secondary endpoints included progression-free survival (PFS), overall survival (OS) and toxicity.

RESULTS

Overall, 17 evaluable patients enrolled. Median age was 60 years (26-85); median number of prior therapy lines, 2 (0-5). ORR was 18%; 3/17 patients achieved objective responses (1 complete, 2 partial responses) (2 spindle cell, 1 chondromyxoid histology), which are ongoing at 28+, 33+ and 34+ months, respectively. Median PFS and OS were 2 and 12 months, respectively. Altogether, 11 patients (65%) experienced adverse events (AEs), including one grade 5 AE. Eight patients (47%) developed an immune-related AE (irAE); with adrenal insufficiency observed in all three responders. Responses occurred in tumors with low tumor mutational burden, low PD-L1 and absent TILs.

CONCLUSION

The ipilimumab and nivolumab combination showed no new safety signals and met its primary endpoint with 18% ORR in advanced, chemotherapy-refractory MpBC. All responses are ongoing at >2 to almost 3 years later. The effect of ipilimumab and nivolumab was associated with exceptional responses in a subset of patients versus no activity. This combination warrants further investigation in MpBC, with special attention to understanding mechanism of action, and carefully designed to weigh against the significant risks of irAEs.

Abstract PS11-14: Advanced precision health resources in the Susan G Komen tissue bank at the IU simon comprehensive cancer center

Background: Understanding how hereditary, lifestyle and demographic risk factors influence the development of breast cancer is critical for its prevention and treatment. For this purpose, the Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center (KTB) serves as the world’s primary repository for normal breast tissue and blood samples from healthy women (~5,500 tissue + blood donors and ~4,500 blood-only donors). In addition, KTB has received mammograms, H&E images and additional longitudinal health and wellness data from its donors via ongoing annual surveys. Whole genome sequencing has also recently been completed on a subset of 500 donors, including ~125 initially healthy donors who later went on to develop breast cancer. To make these disparate, multi-modal data accessible to the larger research community and add advanced precision health analytics capabilities to the KTB database, LifeOmic's Precision Health Cloud (PHC), a secure healthcare-compliant cloud platform, was chosen to host the KTB data moving forward. The PHC provides browsing and querying capabilities across all data including genomic, demographic, histology, donor surveys, and scanned images. Data from donors can be viewed individually as well as analyzed across cohorts of interest. Computation resources, such as informatics workflows and machine learning infrastructure, are available on the same secure environment to leverage the power of cloud computing without having to download large files. This is in addition to visual and custom analytics using Jupyter Notebooks accessible to collaborators.

Methods: We loaded all available KTB data from ~10,000 donors into the PHC. Donor-reported data collected at the time of donation and subsequent follow-up questionnaire responses were loaded as FHIR Observations and Medications in the PHC. Additional imaging and genomic data loaded into the PHC include approximately 12,000 mammogram images, 5,000 H&E images, 5,000 ancestry-informative genotypes and 500 VCF and BAM files from whole genome sequencing. A timeline view of each donor shows data collected from each donation and follow-up surveys. All genetic variants were annotated upon ingestion into the PHC with functional effect on genes, population allele frequency, ClinVar clinical significance and in silico predictions for functional impact.

Results: To demonstrate the utility of KTB data hosted in the PHC, we will show how the PHC can be used to directly analyze genomic and donor-reported data, specifically focusing on the recent whole genome sequencing data from 500 donors. Whole genome sequencing data will be used to calculate the genetic ancestry of each donor compared to their self-reported ancestry and previously predicted ancestry from a 41-SNP ancestry panel. Additionally, we will calculate genomewide breast cancer polygenic risk scores and compare these with the survey-based Tyrer-Cuzick and Gail score risk measures. We will assess how the polygenic risk score further stratifies the donors that have germline pathogenic variants in a known breast cancer gene. For the ~125 sequenced donors that went on to develop breast cancer we will also investigate correlations between family history of cancer, age of diagnosis, prior gynecological history and lifestyle differences. All generated results will remain in the PHC for access by future KTB collaborators to continue to build the utility and value of the KTB data.

Conclusions: We have shown how hosting KTB data in the PHC opens new opportunities for advanced precision health research for breast cancer researchers worldwide. As more specimens and diverse data sets including genomic, longitudinal and imaging information are being tracked and deposited into KTB, this resource will continue to grow to enable diverse research needs.

Citation Format: Steven M Bray, Swee Seong Wong, Baiju G Parikh, Kevin C Wood, Samuel T Rysdyk, Jill E Henry, Natascia Marino, Milan Radovich, Anna Maria V Storniolo. Advanced precision health resources in the Susan G Komen tissue bank at the IU simon comprehensive cancer center [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS11-14.

Abstract PS10-26: An initial safety study of gedatolisib plus cofetuzumab pelidotin for metastatic triple-negative breast cancer

Background: The PI3K pathway is dysregulated in the majority of triple-negative breast cancer (TNBCs), yet single agent inhibition of PI3K in TNBC has minimal clinical activity. We previously reported that PI3K inhibition leads to an immediate compensatory up-regulation of the Wnt pathway. Dual targeting of both pathways is highly synergistic against TNBC models in vitro and in vivo. We initiated a Phase I clinical trial of gedatolisib, a pan-class I isoform PI3K/mTOR inhibitor, and cofetuzumab pelidotin, an antibody-drug conjugate against the cell-surface PTK7 protein (Wnt pathway co-receptor) with an auristatin payload. PTK7 is up-regulated after PI3K inhibition and auristatin is in itself synergistic with gedatolisib providing the potential for a dual mechanism of synergy.

Methods: Dose escalation proceeded using a traditional 3+3 schema with a small expansion cohort at the final dose level to better characterize safety. Participants had metastatic TNBC or ER low (ER and PgR &lt;5%, HER2 negative) breast cancer, and had received at least one prior line of chemotherapy. The primary objective was safety. Secondary endpoints included objective response (ORR), clinical benefit at 18 weeks (CB18), and progression-free survival (PFS). Exploratory analyses probed the association of tumor DNA, RNA, and IHC with clinical efficacy to identify putative biomarkers.

Results: Between January 2018 and January 2020, 18 patients were enrolled in 3 dose cohorts: gedatolisib (qw) & cofetuzumab pelidotin (q3w) 110mg+1.4mg/kg (n=4), 180mg+1.4mg/kg (n=3), and 180mg+2.8mg/kg dose levels (n=11). The median age was 53 years (32-77). Nausea (n=16), anorexia (n=13), fatigue (n=12), and mucositis (n=12) were common but rarely reached &gt;Grade 3 severity (nausea, n=1; fatigue, n=2). Myelosuppression was uncommon (Grade &gt;3 neutropenia, n=2). 16 participants were evaluable for response. 3 achieved a confirmed partial response (PR), and 3 had stable disease (SD). ORR=18.8%. All 3 PRs lasted &gt; 6 months. CB18=31.3%. Median PFS was 2.0 months (95% CI for PFS:1.2-6.2); median OS was 9.5 months (95% CI for OS:4.3-not reached). Correlative analyses of genomic, transcriptomic, and protein biomarkers with response are currently ongoing.

Conclusions: The combination of gedatolisib + cofetuzumab pelidotin for the treatment of metastatic TNBC was found to be well tolerated and demonstrated promising clinical activity. Further investigation of this drug combination in metastatic TNBC is warranted.

Trial Registration: NCT03243331

Citation Format: Milan Radovich, Jeffrey P. Solzak, Bradley A. Hancock, Sunil Badve, Anna Maria V. Storniolo, Tarah J. Ballinger, Bryan P. Schneider, Kathy D. Miller. An initial safety study of gedatolisib plus cofetuzumab pelidotin for metastatic triple-negative breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS10-26.

Association of Circulating Tumor DNA and Circulating Tumor Cells After Neoadjuvant Chemotherapy With Disease Recurrence in Patients With Triple-Negative Breast Cancer: Preplanned Secondary Analysis of the BRE12-158 Randomized Clinical Trial

Importance

A significant proportion of patients with early-stage triple-negative breast cancer (TNBC) are treated with neoadjuvant chemotherapy. Sequencing of circulating tumor DNA (ctDNA) after surgery, along with enumeration of circulating tumor cells (CTCs), may be used to detect minimal residual disease and assess which patients may experience disease recurrence.

Objective

To determine whether the presence of ctDNA and CTCs after neoadjuvant chemotherapy in patients with early-stage TNBC is independently associated with recurrence and clinical outcomes.

Design, Setting, and Participants

A preplanned secondary analysis was conducted from March 26, 2014, to December 18, 2018, using data from 196 female patients in BRE12-158, a phase 2 multicenter randomized clinical trial that randomized patients with early-stage TNBC who had residual disease after neoadjuvant chemotherapy to receive postneoadjuvant genomically directed therapy vs treatment of physician choice. Patients had blood samples collected for ctDNA and CTCs at time of treatment assignment; ctDNA analysis with survival was performed for 142 patients, and CTC analysis with survival was performed for 123 patients. Median clinical follow-up was 17.2 months (range, 0.3-58.3 months).

Interventions

Circulating tumor DNA was sequenced using the FoundationACT or FoundationOneLiquid Assay, and CTCs were enumerated using an epithelial cell adhesion molecule-based, positive-selection microfluidic device.

Main Outcomes and Measures

Primary outcomes were distant disease-free survival (DDFS), disease-free survival (DFS), and overall survival (OS).

Results

Among 196 female patients (mean [SD] age, 49.6 [11.1] years), detection of ctDNA was significantly associated with inferior DDFS (median DDFS, 32.5 months vs not reached; hazard ratio [HR], 2.99; 95% CI, 1.38-6.48; P = .006). At 24 months, DDFS probability was 56% for ctDNA-positive patients compared with 81% for ctDNA-negative patients. Detection of ctDNA was similarly associated with inferior DFS (HR, 2.67; 95% CI, 1.28-5.57; P = .009) and inferior OS (HR, 4.16; 95% CI,1.66-10.42; P = .002). The combination of ctDNA and CTCs provided additional information for increased sensitivity and discriminatory capacity. Patients who were ctDNA positive and CTC positive had significantly inferior DDFS compared with those who were ctDNA negative and CTC negative (median DDFS, 32.5 months vs not reached; HR, 5.29; 95% CI, 1.50-18.62; P = .009). At 24 months, DDFS probability was 52% for patients who were ctDNA positive and CTC positive compared with 89% for those who were ctDNA negative and CTC negative. Similar trends were observed for DFS (HR, 3.15; 95% CI, 1.07-9.27; P = .04) and OS (HR, 8.60; 95% CI, 1.78-41.47; P = .007).

Conclusions and Relevance

In this preplanned secondary analysis of a randomized clinical trial, detection of ctDNA and CTCs in patients with early-stage TNBC after neoadjuvant chemotherapy was independently associated with disease recurrence, which represents an important stratification factor for future postneoadjuvant trials.

Trial Registration

ClinicalTrials.gov Identifier: NCT02101385.

Polygenic risk score for the prediction of breast cancer is related to lesser terminal duct lobular unit involution of the breast

Terminal duct lobular units (TDLUs) are the predominant anatomical structures where breast cancers originate. Having lesser degrees of age-related TDLU involution, measured as higher TDLUs counts or more epithelial TDLU substructures (acini), is related to increased breast cancer risk among women with benign breast disease (BBD). We evaluated whether a recently developed polygenic risk score (PRS) based on 313-common variants for breast cancer prediction is related to TDLU involution in the background, normal breast tissue, as this could provide mechanistic clues on the genetic predisposition to breast cancer. Among 1398 women without breast cancer, higher values of the PRS were significantly associated with higher TDLU counts (P = 0.004), but not with acini counts (P = 0.808), in histologically normal tissue samples from donors and diagnostic BBD biopsies. Mediation analysis indicated that TDLU counts may explain a modest proportion (≤10%) of the association of the 313-variant PRS with breast cancer risk. These findings suggest that TDLU involution might be an intermediate step in the association between common genetic variation and breast cancer risk.

Estimating breast tissue-specific DNA methylation age using next-generation sequencing data

Background

DNA methylation (DNAm) age has been widely accepted as an epigenetic biomarker for biological aging. Emerging evidence suggests that DNAm age can be tissue-specific and female breast tissue ages faster than other parts of the body. The Horvath clock, which estimates DNAm age across multiple tissues, has been shown to be poorly calibrated in breast issue. We aim to develop a model to estimate breast tissue-specific DNAm age.

Methods

Genome-wide DNA methylation sequencing data were generated for 459 normal, 107 tumor, and 45 paired adjacent-normal breast tissue samples. We determined a novel set of 286 breast tissue-specific clock CpGs using penalized linear regression and developed a model to estimate breast tissue-specific DNAm age. The model was applied to estimate breast tissue-specific DNAm age in different breast tissue types and in tumors with distinct clinical characteristics to investigate cancer-related aging effects.

Results

Our estimated breast tissue-specific DNAm age was highly correlated with chronological age (r = 0.88; p = 2.9 × 10⁻³¹) in normal breast tissue. Breast tumor tissue samples exhibited a positive epigenetic age acceleration, where DNAm age was on average 7 years older than respective chronological age (p = 1.8 × 10⁻⁸). In age-matched analyses, tumor breast tissue appeared 12 and 13 years older in DNAm age than adjacent-normal and normal breast tissue (p = 4.0 × 10⁻⁶ and 1.0 × 10⁻⁶, respectively). Both HER2+ and hormone-receptor positive subtypes demonstrated significant acceleration in DNAm ages (p = 0.04 and 3.8 × 10⁻⁶, respectively), while no apparent DNAm age acceleration was observed for triple-negative breast tumors. We observed a non-linear pattern of epigenetic age acceleration with breast tumor grade. In addition, early-staged tumors showed a positive epigenetic age acceleration (p = 0.003) while late-staged tumors exhibited a non-significant negative epigenetic age acceleration (p = 0.10).

Conclusions

The intended applications for this model are wide-spread and have been shown to provide biologically meaningful results for cancer-related aging effects in breast tumor tissue. Future studies are warranted to explore whether breast tissue-specific epigenetic age acceleration is predictive of breast cancer development, treatment response, and survival as well as the clinical utility of whether this model can be extended to blood samples.

Abstract P5-08-16: Molecular landscape of the breasts of women at high risk for breast cancer

Background: Despite advances in breast cancer diagnosis and treatment, there is a critical need to identify the determinants of breast cancer susceptibility in order to define new strategies to target cancer initiation and progression. The Susan G. Komen Tissue Bank at Indiana University (KTB), the only repository worldwide of non-malignant breast samples, can address key scientific questions by examining molecular changes, including epigenetic (DNA methylation) and transcriptomic alterations that occur in breasts of cancer-free women who are considered at high risk for developing breast cancer.

Methods: Disease-free breast tissue cores donated by 80 high-risk (Tyrer-Cuzick lifetime risk ≥20%) and 80 average-risk women were processed for whole methylome (Diagenode MeCap Seq Library and NextSeq 75_sequencing) and whole transcriptome (Illumina TruSeq Stranded mRNA HT Library followed by NextSeq 75_sequencing) profiling. The two groups were matched according to age, racial background, and menopausal status. The cohort included 131 pre-menopausal and 29 post-menopausal women (mean age 38.6, SD 12.1). Frozen breast tissue cores with either abundant or moderate epithelial cellularity were selected. For the gene expression analysis, the reads were mapped to the human genome reference, GRCh38.p12 using the alignment software STAR ver. 2.5.2b and the read counts per gene were obtained using featureCounts ver. 1.6.3. For the evaluation of the epigenetically regulated genes, we focused our investigation on two types of functionally relevant epigenetic panels: the first panel includes 666 cancer-related markers (or pan-cancer) described by Shegafinia et al 2018, and the second panel includes 16 epigenetic markers identified in normal breast tissues-derived cells as connected with breast epithelial cell differentiation*.

Results: In a preliminary analysis, we searched for transcriptomic differences in the breast tissues of high-risk women (N=43) as compared with that of matched average-risk subjects (N=48).The differential expression analysis identified 126 differentially expressed genes (DEGs, FDR&lt;0.05, fold change &gt;2), including 117 upregulated and 9 downregulated in the high-risk group. Interestingly, pathway analysis (Ingenuity Pathway Analysis, IPA v06_01) showed that most of these genes are involved with cancer. The sub-category “tumorigenesis of tissues” as defined by IPA included 71 genes. Through TCGA database analysis, using the UALCAN portal, we searched among our candidate genes for those targets that showed both overexpression and hypomethylation in breast tumors as compared with the normal breast, or vice versa, downregulation and hypermethylation in breast cancer. This pipeline allowed us to identify 17 genes potentially epigenetically regulated and involved in breast cancer susceptibility and the early phases of cancer development. Among those, two genes, FAM83A and PLA2G3, belong to a family of genes previously described as epigenetically dysregulated in multiple cancers (TCGA dataset, and Shegafinia et al 2018) and transform breast epithelial cell in vitro (FAM83A), thus reaffirming robustness of our approach in identifying genes associated with breast cancer risk

Conclusion: The discovery of epigenetically regulated genes associated with breast cancer risk will open the doors to a deeper understanding of the process of cancer initiation and progression. The present study identified 17 gene alterations, two of which are epigenetically regulated in cancer. Our findings highlight an opportunity to address molecular alterations potentially linked with breast cancer susceptibility and risk, using a unique resource of normal breast samples.

*Unpublished data by Dr. H. Nakshatri

Citation Format: Natascia Marino, Rana German, Harikrishna Nakshatri, Ashley Vode, Jun Liu, Jie Huang, Douglas B Rush, Sha Cao, Anna Maria V Storniolo. Molecular landscape of the breasts of women at high risk for breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-08-16.

A Computational Statistics Approach to Evaluate Blood Biomarkers for Breast Cancer Risk Stratification

Breast cancer is the second leading cause of cancer mortality among women. Mammography and tumor biopsy followed by histopathological analysis are the current methods to diagnose breast cancer. Mammography does not detect all breast tumor subtypes, especially those that arise in younger women or women with dense breast tissue, and are more aggressive. There is an urgent need to find circulating prognostic molecules and liquid biopsy methods for breast cancer diagnosis and reducing the mortality rate. In this study, we systematically evaluated metabolites and proteins in blood to develop a pipeline to identify potential circulating biomarkers for breast cancer risk. Our aim is to identify a group of molecules to be used in the design of portable and low-cost biomarker detection devices. We obtained plasma samples from women who are cancer free (healthy) and women who were cancer free at the time of blood collection but developed breast cancer later (susceptible). We extracted potential prognostic biomarkers for breast cancer risk from plasma metabolomics and proteomics data using statistical and discriminative power analyses. We pre-processed the data to ensure the quality of subsequent analyses, and used two main feature selection methods to determine the importance of each molecule. After further feature elimination based on pairwise dependencies, we measured the performance of logistic regression classifier on the remaining molecules and compared their biological relevance. We identified six signatures that predicted breast cancer risk with different specificity and selectivity. The best performing signature had 13 factors. We validated the difference in level of one of the biomarkers, SCF/KITLG, in plasma from healthy and susceptible individuals. These biomarkers will be used to develop low-cost liquid biopsy methods toward early identification of breast cancer risk and hence decreased mortality. Our findings provide the knowledge basis needed to proceed in this direction.

Free Fatty Acids Rewire Cancer Metabolism in Obesity-Associated Breast Cancer via Estrogen Receptor and mTOR Signaling

Obesity is a risk factor for postmenopausal estrogen receptor alpha (ERα)-positive (ER⁺) breast cancer. Molecular mechanisms underlying factors from plasma that contribute to this risk and how these mechanisms affect ERα signaling have yet to be elucidated. To identify such mechanisms, we performed whole metabolite and protein profiling in plasma samples from women at high risk for breast cancer, which led us to focus on factors that were differentially present in plasma of obese versus nonobese postmenopausal women. These studies, combined with in vitro assays, identified free fatty acids (FFA) as circulating plasma factors that correlated with increased proliferation and aggressiveness in ER⁺ breast cancer cells. FFAs activated both the ERα and mTOR pathways and rewired metabolism in breast cancer cells. Pathway preferential estrogen-1 (PaPE-1), which targets ERα and mTOR signaling, was able to block changes induced by FFA and was more effective in the presence of FFA. Collectively, these data suggest a role for obesity-associated gene and metabolic rewiring in providing new targetable vulnerabilities for ER⁺ breast cancer in postmenopausal women. Furthermore, they provide a basis for preclinical and clinical trials where the impact of agents that target ERα and mTOR signaling cross-talk would be tested to prevent ER⁺ breast cancers in obese postmenopausal women. SIGNIFICANCE: These findings show that obesity-associated changes in certain blood metabolites rewire metabolic programs in cancer cells, influence mammary epithelial cell tumorigenicity and aggressiveness, and increase breast cancer risk.

Abstract OT3-06-02: An initial safety study of gedatolisib plus PTK7-ADC for metastatic triple-negative breast cancer

Background: The PI3K pathway is dysregulated in the majority of triple-negative breast cancer (TNBCs). Contrary to the theory of oncogene addiction, single agent inhibition of the PI3K pathway in TNBC has had only modest activity. Our group has demonstrated preclinically that when PI3K is inhibited, an immediate compensatory up-regulation of the Wnt pathway occurs. The Wnt pathway is known known for its role in cancer metastases and can confer resistance to initial PI3K inhibition. Simultaneous dual targeting of both pathways is highly synergistic against TNBC models in vitro and in vivo.

We have initiated a Phase I clinical trial using Gedatolisib (PI3K/mTOR inhibitor) and PTK7-ADC (Wnt pathway) for patients with metastatic TNBC (NCT03243331). Gedatolisib is a pan-class I isoform PI3K/mTOR inhibitor, and PTK7-ADC is an antibody-drug conjugate against the cell-surface PTK7 protein (Wnt pathway co-receptor) with an Auristatin payload. PTK7 is an attractive second target due to its up-regulation after PI3K inhibition and its known overexpression in TNBC. Further data has shown that the PTK7-payload, Auristatin, is in itself synergistic with Gedatolisib. The combination of using both of these drugs suggests a unique concept of “double synergy”. Where Gedatolisib increases the expression of the target of PTK7-ADC leading to one mechanism of synergy, and the Auristatin payload on PTK7-ADC is synergistic with Gedatolisib providing a second mechanism.

Study Design: This is an open-label, Phase I, dose-escalation study with a 3 + 3 cohort design. The trial will enroll 12-18 patients. 3 cohorts of at least 3 patients will receive Gedatolisib (weekly) & PTK-ADC (q3w) at 110mg+1.4mg/kg, 180mg+1.4mg/kg, and 180mg+2.8mg/kg dose levels.

Eligibility Criteria: This trial enrolls patients with metastatic triple negative (ER-, PgR-, HER2-) or low estrogen expressing (ER and PgR &lt;5%, HER2-) breast cancer. Patients must have received at least one prior chemotherapy for advanced disease and have adequate hematologic, renal, and hepatic function. Patients with previously treated CNS involvement are eligible. Patients with uncontrolled diabetes are excluded, given the potential for hyperglycemia with Gedatolisib. Patients must have disease amenable and consent to biopsy for correlative endpoints.

Objectives: The primary objective is to evaluate the safety of Gedatolisib plus PTK7-ADC. The secondary objective is to evaluate efficacy as determined by objective response rate, clinical benefit at 18 weeks, and progression free survival (PFS). Exploratory objectives will evaluate efficacy in patients with genomic aberrations in the PI3K pathway; and association of tumor DNA, RNA, plasma and circulating tumor cell sequencing with clinical efficacy to identify putative biomarkers.

Correlative Sciences: We are collecting matched pre-/post-treatment tumor biopsies and serial blood samples to determine biomarkers of clinical response to inform subsequent trials. We plan to evaluate: 1) PI3K activity; 2) genomic aberrations in the PI3K pathway; 3) baseline PTK7 expression; 4) PTK7 upregulation after Gedatolisib treatment; and 5) mutations in plasma circulating tumor DNA.

Supported by the BCRF, 100 Voices of Hope, Catherine Peachey Foundation, and Pfizer.

Citation Format: Radovich M, Solzak JP, Hancock BA, Storniolo AMV, Schneider BP, Miller KD. An initial safety study of gedatolisib plus PTK7-ADC for metastatic triple-negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr OT3-06-02.

Genetic Ancestry-dependent Differences in Breast Cancer-induced Field Defects in the Tumor-adjacent Normal Breast

PURPOSE

Genetic ancestry influences evolutionary pathways of cancers. However, whether ancestry influences cancer-induced field defects is unknown. The goal of this study was to utilize ancestry-mapped true normal breast tissues as controls to identify cancer-induced field defects in normal tissue adjacent to breast tumors (NATs) in women of African American (AA) and European (EA) ancestry.

EXPERIMENTAL DESIGN

A tissue microarray comprising breast tissues of ancestry-mapped 100 age-matched healthy women from the Komen Tissue Bank (KTB) at Indiana University (Indianapolis, IN) and tumor-NAT pairs from 100 women (300 samples total) was analyzed for the levels of ZEB1, an oncogenic transcription factor that is central to cell fate, mature luminal cell-enriched estrogen receptor alpha (ERα), GATA3, FOXA1, and for immune cell composition.

RESULTS

ZEB1⁺ cells, which were localized surrounding the ductal structures of the normal breast, were enriched in the KTB-normal of AA compared with KTB-normal of EA women. In contrast, in EA women, both NATs and tumors compared with KTB-normal contained higher levels of ZEB1⁺ cells. FOXA1 levels were lower in NATs compared with KTB-normal in AA but not in EA women. We also noted variations in the levels of GATA3, CD8⁺ T cells, PD1⁺ immune cells, and PDL1⁺ cell but not CD68⁺ macrophages in NATs of AA and EA women. ERα levels did not change in any of our analyses, pointing to the specificity of ancestry-dependent variations.

CONCLUSIONS

Genetic ancestry-mapped tissues from healthy individuals are required for proper assessment and development of cancer-induced field defects as early cancer detection markers. This finding is significant in light of recent discoveries of influence of genetic ancestry on both normal biology and tumor evolution.

Serum insulin-like growth factor (IGF)-I and IGF binding protein-3 in relation to terminal duct lobular unit involution of the normal breast in Caucasian and African American women: The Susan G. Komen Tissue Bank

Lesser degrees of terminal duct lobular unit (TDLU) involution, as reflected by higher numbers of TDLUs and acini/TDLU, are associated with elevated breast cancer risk. In rodent models, the insulin-like growth factor (IGF) system regulates involution of the mammary gland. We examined associations of circulating IGF measures with TDLU involution in normal breast tissues among women without precancerous lesions. Among 715 Caucasian and 283 African American (AA) women who donated normal breast tissue samples to the Komen Tissue Bank between 2009 and 2012 (75% premenopausal), serum concentrations of IGF-I and binding protein (IGFBP)-3 were quantified using enzyme-linked immunosorbent assay. Hematoxilyn and eosin-stained tissue sections were assessed for numbers of TDLUs ("TDLU count"). Zero-inflated Poisson regression models with a robust variance estimator were used to estimate relative risks (RRs) for association of IGF measures (tertiles) with TDLU count by race and menopausal status, adjusting for potential confounders. AA (vs. Caucasian) women had higher age-adjusted mean levels of serum IGF-I (137 vs. 131 ng/mL, p = 0.07) and lower levels of IGFBP-3 (4165 vs. 4684 ng/mL, p < 0.0001). Postmenopausal IGFBP-3 was inversely associated with TDLU count among AA (RR_T3vs.T1  = 0.49, 95% CI = 0.28-0.84, p-trend = 0.04) and Caucasian (RR_T3vs.T1 =0.64, 95% CI = 0.42-0.98, p-trend = 0.04) women. In premenopausal women, higher IGF-I:IGFBP-3 ratios were associated with higher TDLU count in Caucasian (RR_T3vs.T1 =1.33, 95% CI = 1.02-1.75, p-trend = 0.04), but not in AA (RR_T3vs.T1 =0.65, 95% CI = 0.42-1.00, p-trend = 0.05), women. Our data suggest a role of the IGF system, particularly IGFBP-3, in TDLU involution of the normal breast, a breast cancer risk factor, among Caucasian and AA women.

Abstract 5054: Transcriptional changes in breast cancer initiation

Background: Identifying the earliest stages of breast cancer carcinogenesis, present well before any clinical signs of disease, is the necessary underpinning of an effective breast cancer prevention strategy. We propose to elucidate transcriptomic changes occurring in the breast tissue during cancer initiation. by analyzing biospecimens donated by women before any clinical sign of sporadic breast tumor (here labeled “susceptible”). In the present work, we report on the transcriptome differences in the microdissected breast compartments (epithelium, stroma and fat) of susceptible versus healthy premenopausal women.

Methods: The specimens were obtained from the Susan G. Komen Tissue Bank at IU Simon Cancer Center. We compared the transcriptome profiles of breast tissues from 7 susceptible and 17 healthy premenopausal women between the age of 34 and 52 years, who were free of breast pathology at the time of donation. Donors in the two experimental groups were matched according to age, racial background and menstrual phase. Differential expression analysis was performed using EdegR. False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure. Ingenuity Pathway Analysis was used to identify relevant signaling pathways. Because circulating hormones variations during menstrual cycle affect the breast epithelium gene expression, we also examined transcriptome differences independently from the menstrual phase.

Results/Discussion: We found 536 transcripts differentially expressed between the two groups (p&lt;0.05). However, only 412 changed independently from the follicular or luteal status. Among these, 130 transcripts (including 1 linRNA) were downregulated, while 282 transcripts (including 6 lincRNAs and 5 miRNAs) were upregulated in the susceptible versus healthy breasts. Among the upregulated genes, we observed three major affected pathways: 1) lipid metabolism, 2) molecular transport, and 3) energy production. When we set a more stringent cutoff (p&lt;0.05, fold change&gt; 2 and FDR&lt;0.2), only 11 genes were differentially expressed between susceptible and healthy controls; these are involved in cellular metabolism (AKR1C1, AKR1C2, and SDR16C5) and cell adhesion and cytoskeleton organization (CNTNAP2 and XIRP2). The transcription repressor ZFP57 was the only downregulated gene (fold change=-29; p=0.0002; FDR=0.09).The study will be soon corroborated with the transcriptome profiling of the other two breast compartments (stroma and fat).

Conclusion: This study shows that earliest alterations in breast cancer initiation affect metabolic pathway as well as transcriptional regulation. Interestingly, cell adhesion signaling may also be dysregulated at this early stage of cancer development. The findings will contribute to our understanding of the mechanisms of cancer initiation, as well as the identification of new therapeutic targets and thus, improvement of preventive interventions.

Citation Format: Natascia Marino, Rana German, Mariah L. Johnson, Xi Rao, Xiaoling Xuei, Jun Wan, Anna Maria V. Storniolo. Transcriptional changes in breast cancer initiation [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 5054.

Abstract A36: Serum insulin-like growth factor (IGF)-I and IGF binding protein-3 in relation to terminal duct lobular unit involution in Caucasian and African American women: The Susan G. Komen Tissue Bank

Background: Insulin-like growth factor (IGF)-I and IGF binding protein (IGFBP)-3 play important roles in carcinogenesis, particularly for breast cancer. However, little is known about whether the IGF system influences histologic characteristics of normal glandular tissue and whether relationships vary by race. Lesser degrees of age-related terminal duct lobular unit (TDLU) involution, as reflected by higher numbers of TDLUs and acini per TDLU, have been associated with higher breast cancer risk. We examined the associations of IGF measures with TDLU involution of normal breast using standardized TDLU measures.

Methods: Among 715 Caucasian and 283 African American (AA) women with normal breast tissue samples from the Komen Tissue Bank, serum concentrations of IGF-I and IGFBP-3 were quantified using enzyme-linked immunosorbent assay (ELISA). Hematoxilyn and eosin-stained tissue sections were assessed for numbers of TDLUs (“TDLU count”) and acini/TDLU. Zero-inflated Poisson regression models with a robust variance estimator were used to estimate associations of IGF-I, IGFBP-3, and IGF-I:IGFBP-3 molar ratio (tertiles) with TDLU count by race and menopausal status, adjusting for potential confounders. We also tested for interactions by race using likelihood ratio tests.

Results: AA (vs. Caucasian) women had higher age-adjusted mean levels of serum IGF-I (137 vs. 131 ng/mL, p=0.07) and lower levels of IGFBP-3 (4165 vs. 4684 ng/mL, p&lt;0.0001); the differences persisted after adjustment for additional covariates including BMI and parity/age at first birth. Postmenopausal IGFBP-3 was inversely associated with TDLU count among both AA (RR T3vs.T1=0.49, 95% CI=0.28-0.84, p-trend=0.04) and Caucasian (RR T3vs.T1=0.63, 95% CI=0.41-0.99, p-trend=0.04) women. In premenopausal women, higher IGF-I:IGFBP-3 ratios were associated with higher TDLU count in Caucasians (OR T3vs.T1=1.33, 95% CI=1.01-1.31, p-trend=0.04) but not in AA (OR T3vs.T1=0.65, 95% CI=0.42-1.00, p-trend=0.05) women. There was no statistically significant interaction by race (p-interaction≥0.10).

Conclusions: Our data suggest the potential role of the IGF system, particularly IGFBP-3, in TDLU involution of the normal breast among both Caucasian and AA women.

Citation Format: Hannah OH, Ruth M. Pfeiffer, Roni T. Falk, Hisani N. Horne, Jackie Xiang, Michael Pollak, Louise A. Brinton, Anna Maria V. Storniolo, Mark E. Sherman, Gretchen L. Gierach, Jonine D. Figueroa. Serum insulin-like growth factor (IGF)-I and IGF binding protein-3 in relation to terminal duct lobular unit involution in Caucasian and African American women: The Susan G. Komen Tissue Bank [abstract]. In: Proceedings of the Tenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2017 Sep 25-28; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2018;27(7 Suppl):Abstract nr A36.

Metastatic breast cancer patients' expectations and priorities for symptom improvement

PURPOSE

Little research has examined cancer patients' expectations, goals, and priorities for symptom improvement. Thus, we examined these outcomes in metastatic breast cancer patients to provide patients' perspectives on clinically meaningful symptom improvement and priorities for symptom management.

METHODS

Eighty women with metastatic breast cancer participated in a survey with measures of comorbidity, functional status, engagement in roles and activities, distress, quality of life, and the modified Patient-Centered Outcomes Questionnaire that focused on 10 common symptoms in cancer patients.

RESULTS

On average, patients reported low to moderate severity across the 10 symptoms and expected symptom treatment to be successful. Patients indicated that a 49% reduction in fatigue, 48% reduction in thinking problems, and 43% reduction in sleep problems would represent successful symptom treatment. Cluster analysis based on ratings of the importance of symptom improvement yielded three clusters of patients: (1) those who rated thinking problems, sleep problems, and fatigue as highly important, (2) those who rated pain as moderately important, and (3) those who rated all symptoms as highly important. The first patient cluster differed from other subgroups in severity of thinking problems and education.

CONCLUSIONS

Metastatic breast cancer patients report differing symptom treatment priorities and criteria for treatment success across symptoms. Considering cancer patients' perspectives on clinically meaningful symptom improvement and priorities for symptom management will ensure that treatment is consistent with their values and goals.

Abstract 4250: Molecular alterations in the breast associated with early menarche

Background: Menarche, the onset of the female menstruation, is a marker of pubertal timing. Age at menarche varies widely between girls and is highly dependent on nutritional status and body fat accumulation. The occurrence of menarche at an early age is linked to an increased risk of several adverse health conditions later in life, such as obesity, type-2 diabetes, breast and endometrial cancer, and cardiovascular disease. Indeed, for every one year decrease in age at menarche (from an average age at menarche of 12.5 years), breast cancer risk is increased by 5%. Several genome wide association studies (GWAS) have identified genetic variants (i.e. in the LIN28B gene) that are associated with early age at menarche, however little is known about the changes occurring in the breast tissue of women with early menarche. We hypothesize that early age at menarche results in permanent molecular alterations in the breast tissue and that those abnormalities may contribute to the tissue’s susceptibility to carcinogens and breast cancer development.

Methods: To test our hypothesis we used the resources available at the Susan G. Komen Tissue Bank at the Indiana University Simon Cancer Center (KTB). We selected histologically normal breast tissue from healthy, young women with either early (age ≤ 10 years) or late menarche (age ≥ 15 years), and matched for age, race, BMI, and menstrual phase. Breast tissue biopsies from these women were microdissected to isolate the breast epithelium and next generation RNA-sequencing was used to generate a transcriptome profile for each sample. Differential expression was performed using DESeq2 in R. The tissue samples were also evaluated using immunostaining.

Results/Conclusions: Preliminary data show significant differences when comparing the transcriptome profiles of the microdissected breast epithelium from the early and late menarche sample cohorts. The tissue from women with early menarche had upregulation of genes associated with defense against oxidative stress and/or infectious bacteria (lactotransferrin [LTF], ceruloplasmin [CP]), cell adhesion, (ITGα11, ITGαX, ITGαM, ITGαL, ITGβ2), immune response (CARD9, LAIR1), and had downregulation of ubiquitination pathways (USP40, AMFR) and lipoprotein metabolism (OSBPL1A, LIPH, PIGN). Immunohistochemical evaluation of markers of oxidative stress (LTF, CP), cell proliferation (Ki67), and immune infiltrates (CD45, CD20, CD8, CD68) is underway. Together, this information will give us the opportunity to better understand early age at menarche as a breast cancer risk factor and advance research for women’s health.

Citation Format: Mariah L. Johnson, Natascia Marino, Anna Maria V. Storniolo, Bradley A. Hancock, Milan Radovich, George E. Sandusky. Molecular alterations in the breast associated with early menarche [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4250. doi:10.1158/1538-7445.AM2017-4250

Association between breast cancer genetic susceptibility variants and terminal duct lobular unit involution of the breast

Terminal duct lobular units (TDLUs) are the predominant source of future breast cancers, and lack of TDLU involution (higher TDLU counts, higher acini count per TDLU and the product of the two) is a breast cancer risk factor. Numerous breast cancer susceptibility single nucleotide polymorphisms (SNPs) have been identified, but whether they are associated with TDLU involution is unknown. In a pooled analysis of 872 women from two studies, we investigated 62 established breast cancer SNPs and relationships with TDLU involution. Poisson regression models with robust variance were used to calculate adjusted per-allele relative risks (with the non-breast cancer risk allele as the referent) and 95% confidence intervals between TDLU measures and each SNP. All statistical tests were two-sided; P < 0.05 was considered statistically significant. Overall, 36 SNPs (58.1%) were related to higher TDLU counts although this was not statistically significant (p = 0.25). Six of the 62 SNPs (9.7%) were nominally associated with at least one TDLU measure: rs616488 (PEX14), rs11242675 (FOXQ1) and rs6001930 (MKL1) were associated with higher TDLU count (p = 0.047, 0.045 and 0.031, respectively); rs1353747 (PDE4D) and rs6472903 (8q21.11) were associated with higher acini count per TDLU (p = 0.007 and 0.027, respectively); and rs1353747 (PDE4D) and rs204247 (RANBP9) were associated with the product of TDLU and acini counts (p = 0.024 and 0.017, respectively). Our findings suggest breast cancer SNPs may not strongly influence TDLU involution. Agnostic genome-wide association studies of TDLU involution may provide new insights on its biologic underpinnings and breast cancer susceptibility.

Tissue-specific Co-expression of Long Non-coding and Coding RNAs Associated with Breast Cancer

Inference of the biological roles of lncRNAs in breast cancer development remains a challenge. Here, we analyzed RNA-seq data in tumor and normal breast tissue samples from 18 breast cancer patients and 18 healthy controls and constructed a functional lncRNA-mRNA co-expression network. We revealed two distinctive co-expression patterns associated with breast cancer, reflecting different underlying regulatory mechanisms: (1) 516 pairs of lncRNA-mRNAs have differential co-expression pattern, in which the correlation between lncRNA and mRNA expression differs in tumor and normal breast tissue; (2) 291 pairs have dose-response co-expression pattern, in which the correlation is similar, but the expression level of lncRNA or mRNA differs in the two tissue types. We further validated our findings in TCGA dataset and annotated lncRNAs using TANRIC. One novel lncRNA, AC145110.1 on 8p12, was found differentially co-expressed with 127 mRNAs (including TOX4 and MAEL) in tumor and normal breast tissue and also highly correlated with breast cancer clinical outcomes. Functional enrichment and pathway analyses identified distinct biological functions for different patterns of co-expression regulations. Our data suggested that lncRNAs might be involved in breast tumorigenesis through the modulation of gene expression in multiple pathologic pathways.

Ages at menarche- and menopause-related genetic variants in relation to terminal duct lobular unit involution in normal breast tissue

Reduced levels of terminal duct lobular unit (TDLU) involution, as reflected by higher numbers of TDLUs and acini per TDLU, have been associated with higher breast cancer risk. Younger age at menarche and older age at menopause have been previously related to lower levels of TDLU involution. To determine a possible genetic link, we examined whether single-nucleotide polymorphisms (SNPs) previously established in genome-wide association studies (GWAS) for ages at menarche and menopause are associated with TDLU involution. We conducted a pooled analysis of 862 women from two studies. H&E tissue sections were assessed for numbers of TDLUs and acini/TDLU. Poisson regression models were used to estimate associations of 36 menarche- and 21 menopause-SNPs with TDLU counts, acini counts/TDLU, and the product of these two measures, adjusting for age and study site. Fourteen percent of evaluated SNPs (eight SNPs) were associated with TDLU counts at p < 0.05, suggesting an enrichment of associations with TDLU counts. However, only menopause-SNPs had >50 % that were either significantly or nonsignificantly associated with TDLU measures in the directions consistent with their relationships shown in GWAS. Among ten SNPs that were statistically significantly associated with at least one TDLU involution measure (p < 0.05), seven SNPs (rs466639: RXRG; rs2243803: SLC14A2; rs2292573: GAB2; rs6438424: 3q13.32; rs7606918: METAP1D; rs11668344: TMEM150B; rs1635501: EXO1) were associated in the consistent directions. Our data suggest that the loci associated with ages at menarche and menopause may influence TDLU involution, suggesting some shared genetic mechanisms. However, larger studies are needed to confirm the results.

Circulating sex hormones and terminal duct lobular unit involution of the normal breast

BACKGROUND

Terminal duct lobular units (TDLU) are the predominant source of breast cancers. Lesser degrees of age-related TDLU involution have been associated with increased breast cancer risk, but factors that influence involution are largely unknown. We assessed whether circulating hormones, implicated in breast cancer risk, are associated with levels of TDLU involution using data from the Susan G. Komen Tissue Bank (KTB) at the Indiana University Simon Cancer Center (2009-2011).

METHODS

We evaluated three highly reproducible measures of TDLU involution, using normal breast tissue samples from the KTB (n = 390): TDLU counts, median TDLU span, and median acini counts per TDLU. RRs (for continuous measures), ORs (for categorical measures), 95% confidence intervals (95% CI), and Ptrends were calculated to assess the association between tertiles of estradiol, testosterone, sex hormone-binding globulin (SHBG), progesterone, and prolactin with TDLU measures. All models were stratified by menopausal status and adjusted for confounders.

RESULTS

Among premenopausal women, higher prolactin levels were associated with higher TDLU counts (RRT3vsT1:1.18; 95% CI: 1.07-1.31; Ptrend = 0.0005), but higher progesterone was associated with lower TDLU counts (RRT3vsT1: 0.80; 95% CI: 0.72-0.89; Ptrend < 0.0001). Among postmenopausal women, higher levels of estradiol (RRT3vsT1:1.61; 95% CI: 1.32-1.97; Ptrend < 0.0001) and testosterone (RRT3vsT1: 1.32; 95% CI: 1.09-1.59; Ptrend = 0.0043) were associated with higher TDLU counts.

CONCLUSIONS

These data suggest that select hormones may influence breast cancer risk potentially through delaying TDLU involution.

IMPACT

Increased understanding of the relationship between circulating markers and TDLU involution may offer new insights into breast carcinogenesis. Cancer Epidemiol Biomarkers Prev; 23(12); 2765-73. ©2014 AACR.

Next-generation transcriptome sequencing of the premenopausal breast epithelium using specimens from a normal human breast tissue bank

Introduction

Our efforts to prevent and treat breast cancer are significantly impeded by a lack of knowledge of the biology and developmental genetics of the normal mammary gland. In order to provide the specimens that will facilitate such an understanding, The Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center (KTB) was established. The KTB is, to our knowledge, the only biorepository in the world prospectively established to collect normal, healthy breast tissue from volunteer donors. As a first initiative toward a molecular understanding of the biology and developmental genetics of the normal mammary gland, the effect of the menstrual cycle and hormonal contraceptives on DNA expression in the normal breast epithelium was examined.

Methods

Using normal breast tissue from 20 premenopausal donors to KTB, the changes in the mRNA of the normal breast epithelium as a function of phase of the menstrual cycle and hormonal contraception were assayed using next-generation whole transcriptome sequencing (RNA-Seq).

Results

In total, 255 genes representing 1.4% of all genes were deemed to have statistically significant differential expression between the two phases of the menstrual cycle. The overwhelming majority (221; 87%) of the genes have higher expression during the luteal phase. These data provide important insights into the processes occurring during each phase of the menstrual cycle. There was only a single gene significantly differentially expressed when comparing the epithelium of women using hormonal contraception to those in the luteal phase.

Conclusions

We have taken advantage of a unique research resource, the KTB, to complete the first-ever next-generation transcriptome sequencing of the epithelial compartment of 20 normal human breast specimens. This work has produced a comprehensive catalog of the differences in the expression of protein-coding genes as a function of the phase of the menstrual cycle. These data constitute the beginning of a reference data set of the normal mammary gland, which can be consulted for comparison with data developed from malignant specimens, or to mine the effects of the hormonal flux that occurs during the menstrual cycle.

Characterizing the heterogeneity of triple-negative breast cancers using microdissected normal ductal epithelium and RNA-sequencing

Triple-negative breast cancers (TNBCs) are a heterogeneous set of tumors defined by an absence of actionable therapeutic targets (ER, PR, and HER-2). Microdissected normal ductal epithelium from healthy volunteers represents a novel comparator to reveal insights into TNBC heterogeneity and to inform drug development. Using RNA-sequencing data from our institution and The Cancer Genome Atlas (TCGA) we compared the transcriptomes of 94 TNBCs, 20 microdissected normal breast tissues from healthy volunteers from the Susan G. Komen for the Cure Tissue Bank, and 10 histologically normal tissues adjacent to tumor. Pathway analysis comparing TNBCs to optimized normal controls of microdissected normal epithelium versus classic controls composed of adjacent normal tissue revealed distinct molecular signatures. Differential gene expression of TNBC compared with normal comparators demonstrated important findings for TNBC-specific clinical trials testing targeted agents; lack of over-expression for negative studies and over-expression in studies with drug activity. Next, by comparing each individual TNBC to the set of microdissected normals, we demonstrate that TNBC heterogeneity is attributable to transcriptional chaos, is associated with non-silent DNA mutational load, and explains transcriptional heterogeneity in addition to known molecular subtypes. Finally, chaos analysis identified 146 core genes dysregulated in >90 % of TNBCs revealing an over-expressed central network. In conclusion, use of microdissected normal ductal epithelium from healthy volunteers enables an optimized approach for studying TNBC and uncovers biological heterogeneity mediated by transcriptional chaos.

Abstract P1-03-02: “Normal” tissue adjacent to breast cancer is not normal

Background: Gene expression data from pancreatic cancer, histologically normal tissue adjacent to the cancer and normal pancreas reveals that adjacent normal has already acquired a number of transcriptional alterations and is not, therefore, an appropriate baseline for comparison with cancers. (Gadaleta et al., 2011) The purpose of this study was to determine if this is also the case for breast cancer and, if so, to identify the differences in gene expression between adjacent normal and normal breast.

Methods: RNA-Seq data from breast cancer and adjacent normal was downloaded from the TCGA (The Cancer Genome Atlas) data portal. The epithelia from 20 frozen tissue cores from healthy premenopausal donors to the Susan G. Komen for the the Cure® Tissue Bank at the IU Simon Cancer Center were microdissected and the RNA isolated. RNA-seqeuncing was carried out using the Life Technologies SOLiD Platform. RPKM gene expression values from TCGA and sequencing of the Komen normal tissues were merged, quantile normalized, and batch effect corrected. Normalization and differential gene expression was performed using Partek Genomics Suite.

Results: Principal component analysis (PCA) reveals complete separation between adjacent normal and healthy normal breast tissue. Setting a maximum FDR (false discover rate) of 5%, 2239 genes are differentially expressed between adjacent normal and healthy normal. Ingenuity pathway analysis reveals that the Fos, Jun and TGFbeta pathways are active in the adjacent normal.

Conclusions: Tissue adjacent to a primary breast cancer is not normal when using healthy breast tissue as a comparator. As RNA-Seq data is digital, it is possible to quantify the changes in gene expression starting from healthy normal to normal adjacent to tumor to tumor. Increasing and decreasing gene expression values provide clues to the fundamental molecular changes occurring in histologically normal appearing adjacent tissue. The differences in gene expression we have identified are some of the earliest changes in breast carcinogenesis and provide insight into the etiology of this disease and, potentially, its prevention.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P1-03-02.

Abstract LB-409: Network analysis of RNA-seq data comparing triple negative breast cancer to normal breast tissues

Introduction: Triple-negative breast cancer (TNBC) accounts for 15% of all breast cancers and results in disproportionally higher mortality compared to other breast cancers. Moreover, there is a paucity of therapies for this subtype of breast cancer resulting primarily from an inadequate understanding of the transcriptional differences that differentiate TNBC from normal breast. Using next-generation RNA-seq, we embarked on a study to compare the transcriptomes of TNBC and normal breast to comprehensively identify dysregulated networks, pathways, transcription factors, and high connectivity drug targets that can be exploited for therapeutic discovery. Methods: cDNA libraries from 10 normal breast tissues from the Susan G. Komen Tissue Bank at the IU Simon Cancer Center and 10 TNBC tumors were sequenced on an Applied Biosystems (ABI) SOLiD3 sequencer. Mapping of reads to the human genome (hg18) was performed using ABI BioScope 1.2; differential gene expression was analyzed using Partek Genomics Suite; and network, pathway, and transcription factor analysis was performed using Ingenuity Systems iReport and IPA 9.0. Results: Canonical pathway analysis revealed highly elevated and enriched expression in BRCA/DNA repair pathways, PI3K/AKT, and integrin signaling. Particularly, targeting BRCA/DNA repair pathways with PARP inhibitors has demonstrated some clinical success. Our pathway analysis reveals additional targets: ATM, CHK1/2, & PLK1 that are highly overexpressed and are integral to the BRCA pathway. To determine key regulators of our dataset, we employed IPA's transcription factor (TF) analysis that utilizes a literature knowledge base to identify TFs that explain a set of differential expression data, and classifies them as either activated or inhibited. We observed that TP53, RB1, & CDKN2A were significantly inhibited. This is congruent with current literature showing that TP53 & RB1 as the most predominantly mutated genes in TNBC. In terms of activation, TBX2 and c-MYC were significantly activated in our dataset, suggesting a highly pro-tumorigenic transcriptional programme. In addition, RNA-seq detects pre-miRNAs. When integrated into the analysis, the top ranked network reveals a large set of dysregulated miRNAs secondary to inhibited TP53. When looking at druggable kinases, we performed a connectivity analysis to determine major hub proteins. Our top three kinases were SRC, IKBKE, and AKT1. Of note AKT inhibitors have recently entered early phase clinical trials in breast cancer. Conclusions: Network analysis reveals a concerted programme of proteins and transcription factors that drive a highly pro-tumorigenic phenotype revolving around nonfunctional TP53, and upregulated PI3K/AKT & DNA damage repair pathways. The analysis reveals additional DNA damage repair proteins in addition to PARP and highly connected kinases as potential drug targets for TNBC.

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 LB-409. doi:1538-7445.AM2012-LB-409

Abstract 3322: Phenotypic plasticity in the normal breast

Metaplasia is observed in almost all epithelial cancers. The origins of metaplasia are obscure although chronic inflammation is thought to be one etiology. We present data that suggests that an origin of metaplasia is the normal resident stem cell population. Methods: Starting from 10 gauge tissue cores of normal breast donated to the Komen Tissue Bank, 28 normal mammary epithelial (HME) and 33 normal stromal (HMS) cell lines were established using an organoid isolation method after digestion with enzymes for 24 hours. The HME cell lines were characterized by immunohistochemistry (IHC). Ploidy was assayed. Cellular morphology was observed both on two-dimensional and in three-dimensional culture systems. The HME cells were subjected to FACS analysis using multiple antibodies. Results: 96.9% of early passage cells are diploid. The HME cells express vimentin, CK 5/6, p63, CD 10, CK 18, and HER-1 when grown on two dimensional plastic surfaces. Cells placed in the center of a sandwich of Matrigel uniformly make spheres 37mm-325mm in diameter. Hematoxylin and eosin staining of the formalin-fixed and paraffin-embedded sections of these spheres reveal keratinized squamous differentiation. When the cells are grown on Laminin, Collagen Type IV, or Fibronectin surfaces multiple cell types are observed including osteoclasts, distinguished by the presence of Tartrate Resistant Acid Phospatase; and chondrocytes, confirmed by staining with Alcian Blue. Other cells with a spindle-shape and cytoplasmic vacuoles turn a dark reddish-brown color when stained with Oil Red O, characteristics of adipocytes. In other areas of the culture, the cells form a syncitium and they express the protein MyoD, a marker of immature muscle. Finally, there are numerous cells with long, dendritic processes. These cells express Nestin, glial fibrillary acidic protein (GFAP), and beta-III tubulin. Using FACS, the HME cells were found to be CD49f positive and EpCAM negative. Multiple nucleoli were confirmed using anti-Nucleostemin IHC. Conclusions: Phenotypic plasticity is common to all the HME cell lines characterized to date. Differentiation into cells of mesodermal and ectodermal origin, CD49+/EpCAM- by FACS, and the presence of multiple nucleoli suggest that the isolated cells are a multipotent/stem cell residing in the normal adult breast. These cells, through a series of yet to be elucidated events, may be the cells of origin of both benign and malignant metaplasia observed in breast lesions.

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 3322. doi:1538-7445.AM2012-3322

P5-21-02: The Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center: The Source for Normal Breast Tissue and Biospecimens

Background

Our efforts to prevent and treat breast cancer are significantly impeded by a lack of knowledge of the biology and developmental genetics of the normal mammary gland. This ignorance has been the consequence of the lack of access to richly annotated, high quality normal breast specimens. The Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center (KTB) was established expressly to remedy this deficiency. The KTB is a repository of specimens from volunteer donors with no clinical evidence of breast malignancy. The Bank's mission is to make available specimens that will enable an understanding of the developmental biology of the normal breast, to provide insight into breast oncogenesis, and to provide a normal control for breast cancer research. The purpose of this presentation is to increase the awareness of this unique and rich research resource and to actively solicit the use of its specimens.

Methods: The KTB has been prospectively banking fresh frozen breast tissue since mid-2006. Coincident with the tissue donation two tubes of blood are obtained, which are processed for lymphocyte DNA, serum and plasma. These specimens are richly annotated with detailed information regarding the donors’ reproductive history, medical history, family history, and medications. Standard Operating Procedures have been constructed so as to control, limit and identify potential sources of bias. All of this information is recorded in an Oracle-based, searchable database.

Results: As of June 2011, the KTB and its predecessor bank, Mary Ellen's Bank, have available fresh frozen breast tissue (10 gauge cores) from 1469 donors; formalin-fixed, paraffin-embedded tissue from 1055; DNA from 7507; serum from 2382; and plasma from 3771 donors. The KTB has also established 28 epithelial and 33 stromal cell lines from the cores; 4 of the epithelial cell lines have been immortalized using hTERT. Donors range in age from 18–86 years of age. 9% of donors to the KTB describe themselves as Hispanic/Latino. 5.2% of donors are Black or African-American. Using the Gail Risk Model, there is a bimodal distribution of life-time breast cancer risk among the donors: the largest peak is at 10% and a smaller one at 18%.

Conclusions: The KTB is a unique and invaluable research resource which is now open for business and accessible to researchers across the globe. We encourage researchers to avail themselves of this unique tissue resource and to also acquaint themselves with other sources of healthy breast tissue, i.e., the Love/Avon Army of Women [http://www.armyofwomen.org/].

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-21-02.

Abstract PD01-08: Decoding the Transcriptional Landscape of Triple-Negative Breast Cancer Using Next-Generation Whole Transcriptome Sequencing

Background: Triple-negative breast cancer (TNBC) has been plagued by the absence of targeted therapies. Discovery of therapeutic targets in TNBC has in part, been hampered by an inadequate understanding of the transcriptional biology of the normal breast as an optimal comparator. Using next-generation sequencing, we embarked on a study to compare the transcriptomes of TNBC and normal breast to comprehensively identify novel targets by analyzing all full length transcripts expressed in these tissues.

Methods: Normal breast tissues from healthy pre-menopausal volunteers with no history of disease were procured from the Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center. To eliminate bias from stromal tissue, normal tissues were laser capture microdissected for ductal epithelium. cDNA libraries from 10 TNBC tumors and 10 normal breast tissues were sequenced on an Applied Biosystems (AB) SOLiD3 sequencer using 50bp fragment runs. For gene expression, mapping of reads to the genome was performed using the AB BioScope 1.2 Pipeline and outputs imported into Partek Genomics Suite for analysis. In Partek, mapped reads were cross-referenced against known genes from the UCSC database followed by statistical comparison of RPKM values for each gene between TNBC and normal. Dimensionality reduction analyses (PCA & Hierarchical clustering) and identification of Novel Transcribed Regions were also performed in Partek, whereas construction of gene networks was performed using Ingenuity Pathway Analysis. To identify gene fusions, partially mapped reads were interrogated utilizing a novel algorithm that searched for reads spanning exons from two different genes. Fusions that were supported by at least 3 reads (of which 2 had to be unique) were considered candidates and were subsequently validated. Results/Discussion: Sequencing produced 1.1 billion reads equaling 57.3GB of data of which 36.0GB (63%) mapped to the human genome. In comparing RPKM values between TNBC and Normal, we report 7140 RefSeq Genes, 22 pre-miRNAs, 109 lincRNA exons, and 15 ultraconserved regions that were differentially expressed between these tissues (FDR&lt;0.01). Biological interpretation of these results reveals upregulation of genes and miRNAs involved in DNA repair, angiogenesis, and inhibitors of Estrogen Receptor-alpha. Some previous drug targets (e.g. EGFR and c-kit) were not found to be upregulated here which may explain lack of clinical success to date. Conversely, PARP was significantly upregulated and early trial results suggest a strong signal for efficacy with inhibition of PARP. We also surveyed the genome for Novel Transcribed Regions (NTRs), defined as areas of significant transcription where no annotated gene is present. When comparing between TNBC and Normal, we report 6408 NTRs to be differentially expressed (FDR&lt;0.01). Lastly, when analyzing the dataset for gene fusions, we identified several gene fusions in the TNBC samples, though no individual fusion was present in more than one sample.

Conclusion: We report an extensive comparison of the transcriptomes of TNBC and normal ductal epithelium. We identified numerous genes previously unknown to be dysregulated in TNBC that can be utilized for therapeutic discovery.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr PD01-08.

Abstract 2216: Next-generation whole transcriptome sequencing of triple-negative breast tumors and normal tissues

Background: Triple-negative breast cancer (TNBC) disproportionally affects pre-menopausal women and women of African-American descent, and has been plagued by the absence of targeted therapies leading to poor survival. The paucity of therapeutic targets in TNBC impels us to utilize new technologies that can determine novel targets on a global scale. Using next-generation sequencing, we embarked on a study to analyze the whole transcriptomes of TNBC tumors compared to normal breast tissues in order to comprehensively identify novel targets by analyzing all full length transcripts expressed in these tissues.

Methods: Normal breast tissues from healthy pre-menopausal volunteers with no history of disease were procured from the Susan G. Komen for the Cure® Tissue Bank at the IU Simon Cancer Center. To eliminate bias from stromal tissue, epithelial cells were laser capture microdissected and RNA extracted from captured cells. cDNA libraries from 10 TNBC tumors and 10 normal breast tissues were subsequently sequenced on an ABI SOLiD3 sequencer using a 50bp fragment run. For gene expression, mapping of reads to the human genome was performed using the ABI Whole Transcriptome Pipeline and outputs were imported into Partek Genomics Suite for analysis. To analyze for gene fusions, reads were mapped to the genome using the SOLiD Analysis Pipeline Tool, followed by an alignment to Refseq to map reads crossing exon-exon junctions. A composite transcriptome was formed from areas of the genome with significant expression (17% of the genome sequence) and served as a concise search space for identifying fusions. Reads not mapping to the genome or to RefSeq (a rich source of fusion reads) were then mapped to the composite transcriptome using BLAT to facilitate a highly accurate split-read alignment. Using a custom developed pipeline, reads that spanned transcribed regions from two different chromosomes, or to loci farther than 200kb apart on the same chromosome, were considered as candidate fusions.

Results/Discussion: Sequencing of the 10 TNBC tumors and 10 normal samples produced 1.1 billion reads equaling 58.15GB of data. Mapping of the reads to the genome revealed 1.6 million transcribed regions (exons) of significant expression. A preliminary analysis of gene expression shows 55.2% of the transcribed loci to have significant differential expression between tumor and normal. Network-node, non-coding RNA, and statistical analyses are currently ongoing. In a further interim analysis, we bioinformatically identified several interchromosomal fusions that were present in a majority of the tumors but were absent in the normal samples. RT-PCR validation of these candidate fusions in a larger validation cohort of TNBC tumors and normal breast tissues is ongoing. A multitude of additional analyses including but not limited to: novel transcripts, alternative splicing, and presence of viral genes are also planned.

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 2216.