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Background: The explosion in new treatment options targeting immune checkpoints, HER signaling, DNA repair deficiency, AKT, and other pathways calls for updated breast cancer subtypes beyond HR and HER2 status to predict which patients will respond to which treatments. Here we leverage the I-SPY 2 TRIAL biomarker program over the past 8 years across 10 treatment arms to elucidate a minimal set of biomarkers that may improve response prediction in a modern treatment context, and to investigate which new patient phenotypes are identified by these response-predictive biomarkers. Methods: 986 patients were considered in this analysis. Treatments included paclitaxel alone (or with trastuzumab (H) in HER2+) or combined with investigational agents: veliparib/carboplatin (VC); neratinib; MK2206; ganitumab; ganetespib; AMG386; TDM1/pertuzumab (P); H/P; and pembrolizumab (Pembro). 24 prospectively defined, mechanism-of-action and pathway-based expression and phospho-protein signatures/biomarkers assayed from pre-treatment biopsies were previously found to be predictive in a particular agent/arm in pre-specified analysis. Here we evaluate these biomarkers in all patients. We assessed association between each biomarker and response in the population as a whole and within each arm and HR/HER2 subtype using a logistic model. To identify optimal dichotomizing thresholds for select biomarkers, 2-fold cross-validation was repeated 500 times. Our analysis is exploratory and does not adjust for multiplicities. Results: Our initial set of 24 predictive biomarkers reflects DNA repair deficiency (n=2), immune activation (n=7), ER signaling (n=2), HER2 signaling (n=4), proliferation (n=2), phospho-activation of AKT/mTOR (n=2), and ANG/TIE2 (n=1) pathways, among others. Biomarkers reflecting similar biology are correlated and cluster together. We make use of this correlation structure to reduce the dimensionality of the biomarker set to five predictive signals: proliferation, DNA repair deficiency (DRD), immune-engaged (Immune+), luminal/ER (lum), and HER2-activated. These biomarkers, when dichotomized, identify patient groups with differential predicted sensitivities to I-SPY 2 agents and are present at different proportions within receptor subtypes. For instance, in the HER2- subset, Immune+/DRD+ patients are predicted sensitive to both VC and Pembro, and account for 39% of TN, but only 12% of HR+HER2-. On the other end of the spectrum, only 17% of TN are Immune-/DRD-, compared to the majority (56%) of HR+HER2-. There are also subsets of patients positive for only one marker. For the HER2+ subset, 67% are HER2-activated+, and 25% lum+; of these HER2-activated+ patients are more likely to be Immune+ (44%), vs 23% in lum+. HER2-activated+/Immune+ patients have higher predicted sensitivity to HER2-targeted agents than lum+ or Immune- patients. In all, these molecular phenotypes predict sensitivity to one or more I-SPY 2 investigational agents for 75% of the ˜ 1000 patients. Conclusion: Molecular phenotypes reflecting proliferation, immune engagement, HER2-activation, luminal/ER-signaling, and DNA repair deficiency may provide a roadmap to guide treatment prioritization for emerging therapeutics. Citation Format: Wolf DM, Yau C, Wulfkuhle J, Petricoin E, Campbell M, Brown-Swigart L, Hirst G, Asare S, Zhu Z, Lee EP, Delson A, Pohlmann P, I-SPY 2 TRIAL Consortium, Hylton N, Liu MC, Symmans F, DeMichele A, Yee D, Berry D, Esserman L, van 't Veer L. Identifying breast cancer molecular phenotypes to predict response in a modern treatment landscape: Lessons from ˜1000 patients across 10 arms of the I-SPY 2 TRIAL [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 P3-10-02.

Background: Triple-negative breast cancer (TNBC) accounts for approximately 10 to 15% of all breast cancer cases. The management of TNBC cases will significantly improve once molecular mechanisms specific to TNBC cells will be identified and treated accordingly. Evidence suggests that TNBC cells display deregulated kinase-dependent signaling cascades that differ from non-triple-negative breast cancer cells. We hypothesized that uniquely divergent phospho-circuits could be distinguished between TNBC and non-TNBC cell lines. By revealing such unique, dysfunctional phospho-signaling network, our long-term objective is to identify kinases that underpin triple-negative breast cancer development, and can be inhibited using targeted therapy. Methods: The kinome activity of TNBC and non-TNBC cell lines was identified (HCC70, MDA-MB-231, MDA-MB-436 compared to AU565, MCF-7, T47D). The functional phospho-signature of each breast cancer cell was analyzed using a high throughput experimental platform that monitors the level of activity of myriad kinases at once. This technique uses 242 phospho-sensing probes and 78 controls in an aqueous-based assay to simultaneously and directly measure the phospho-catalytic activity of phosphorylating enzymes in cell lysates. We mapped the most significantly deranged phospho-signaling cascades and the related kinases. Results: Using 6 cell lines tested under various conditions, we generated 72 phospho-signatures, out of a total of 23,040 data points. After validating the repeatability and robustness of the assay, the kinase activity signature of each breast cancer cell line was analyzed and compared to each other using unsupervised hierarchical clustering. The phospho-sensing assay revealed the heterogeneity of kinase activity networks among breast cancer cells. These data also established that phospho-signaling cascades related to AKT, ERK, and SRC kinases were differentially altered in TNBC and non-TNBC cell lines. Conclusions: We successfully identified unique phospho-circuits of TNBC and non-TNBC cell lines. Our goal is now to test whether specific kinase inhibitors can efficiently kill or prevent the growth of TNBC cell lines in culture and animal models. We will expand our approach into a high-content, functional kinome-screening platform to characterize the phospho-fingerprint of breast cancer cells and tissues, and explore the druggable, kinase-dependent mechanisms critical to triple-negative breast tumors. Citation Format: Bo Pan, Miki Mori, Pei Rong Evelyn Lee, Marij Hartog, Qiang Sun, Laura van 't Veer, Jean-Philippe Coppe. Functional mapping of the oncogenic kinome activity of triple-negative breast cancer cells [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 P2-05-09.

Background: Veliparib, an inhibitor of Poly(ADP-ribose) polymerase (PARPi), in combination with DNA-damaging agents showed significant efficacy, especially in triple negative breast cancer (TNBC) patients. However, in I-SPY 2, approximately 42% of TNBC did not optimally respond to the veliparib based treatment. To exert therapeutic effect, drugs such as veliparib or the DNA damaging agent carboplatin must reach cancer cells at an adequate concentration. Differences within the microenvironment of the tumor (e.g. reduced vascular density and leaky endothelium) are responsible for variability in the uptake and distribution of the drug in the tumor. We hypothesize that heterogeneous or insufficient drug concentrations in the solid tumor lead to inadequate response to PARPi in some TNBC patients. First we performed a mouse xenograft study to determine the penetration and distribution of veliparib and carboplatin in TNBC tumors in mice. Methods: 1*106 MDA.MB.231, HCC70 or MDA.MB.436 cells were injected bilaterally into mamamary fat pad of a total of 36 Beige SCID mice. When the tumors exceeded 200 mm3, veliparib (20mg/kg or 60mg/kg) or placebo was orally administered 3 times daily for 3 days + Carboplatin 60mg/kg on day 1+2. These doses and dosing schedules were estimated to result equivalent plasma and tumor concentrations in mice compared to the doses currently used in clinical trials. Mice were euthanized 3 hours after the last dose of veliparib and tumors, and muscle tissues were obtained. In addition, control tissues were spiked with a broad range of concentrations of veliparib. The spatial distribution of the drugs in the tumor tissue was measured using Matrix-assisted laser desorption/ ionization mass spectrometric imaging (MALDI). The protonated molecular ion at m/z 245.1 was used to construct 2D ion maps of the tissue showing relative quantitation of drug levels. H&E staining was performed to characterize the tumors. Results: Veliparib in control tissues was detected at very low concentrations with a range of detection between 100 fmol-1nmol. After dosing, veliparib penetrates into the tumors and was detectable at both dose levels. However, drug distribution within the tumors was observed to be inhomogeneous. In spots where the drug accumulated, necrosis was observed. Veliparib accumulated in spots in the tumor and near the rim of the tumor. Differences between cell lines were observed, with the largest accumulation at the rim in BRCA mutated cells. Conclusions: Veliparib can be measured using MALDI with good specificity and sensitivity and using concentrations equivalent to patients. TNBC tumors show largely heterogeneous distribution of PARPi, with accumulation in the pushing margings of the tumor. Future analyses will determine whether this heterogeneity in drug distribution explains variability in response to PARPi therapies. Citation Format: Imke H Bartelink, Brendan Prideaux, Byron Hann, Gregor Krings, Jean-Phillippe Coppe, Lamorna Swigart-Brown, Pei Rong Evelyn Lee, Laura Esserman, Douglas Yee, Denise Wolf, Rada M Savic, Laura van t Veer. Spatial distribution of veliparib measured by matrix assisted laser desorption ionization mass spectrometry in triple negative breast cancer tumors [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 P6-11-02.

Background: Previous studies suggest that within the triple positive HR+HER2+ subtype, patients classified as BluePrint (BP) Luminal subtype are more responsive to pertuzumab and trastuzumab (P/H) as opposed to trastuzumab (H) alone. In the I-SPY2 TRIAL, HER2-targeted treatment arms include H, P/H, neratinib (N), and T-DM1/Pertuzumab (T-DM1/P); and patients were classified by BP molecular subtyping in addition to conventional receptors. We evaluated BP subtype as a predictor of response in HR+HER2+ patients and assessed pathway differences between BP molecular subtypes. Methods: 125 HR+HER2+ patients (N: 42; P/H: 29, T-DM1/P: 35; H: 19) with pre-treatment Agilent microarrays and BP subtype assignments were considered. We assess association between BP subtypes and pCR using Fisher's exact test. To identify genes associated with BP Luminal vs. BP HER2 subtype, we (1) apply a Wilcoxon rank sum test and (2) fit a logistic model, with the Benjamini-Hochberg (BH) multiple testing correction (BH p Results: Of the 125 HR+HER2+ patients, 71 were BP HER2-type and 50 were BP Luminal-type. The distribution of pCR rates in BP Luminal/ HER2 subtypes are as follows: Distribution of pCR rates in BP Luminal/ HER2 subtypes by treatment armN (n = 40)P/H (n = 29)T-DM1/P (n = 34)H (n = 18)All arms (n = 121)BP Luminal (n = 50)0 / 9 (0%)1 / 12 (8.3%)2 / 16 (12.5%)1 / 13 (7.7%)4 / 50 (8%)BP HER2 (n = 71)12 / 31 (38.7%)13 / 17 (76.5%)15 / 18 (83.3%)1 / 5 (20%)41 / 71 (57.7%)Odds Ratio6.1; p = 0.12730.2; p = 0.00048429.6; p = 8.60E-052.8; p = 0.49015.3; p = 1.04E-08 In a whole transcriptome analysis, 1725 genes were differentially expressed. By DAVID enrichment analysis, the most significantly enriched pathways were related to immune function, with the BP HER2 subgroup showing higher expression. Conclusion: Our analysis suggests that HR+HER2+ BP Luminal subtype is associated with lower response rates to HER2-targeted agents, including P/H, and may need an alternative strategy. BP HER2 subtype appears associated with higher expression of immune-related genes, relative to BP Luminal; and suggests that immune signaling may contribute to HER2-targeted therapy sensitivity. Citation Format: Pei Rong Evelyn Lee, Zelos Zhu, Denise Wolf, Christina Yau, William Audeh, Annuska Glas, Lamorna Brown-Swigart, Gillian Hirst, Angela DeMichele, I-SPY 2 TRIAL Investigators, Laura Esserman, Laura van 't Veer. BluePrint Luminal subtype predicts non-response to HER2-targeted therapies in HR+/HER2+ I-SPY 2 breast cancer patients [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 2612.

Triple-negative breast cancer (TNBC) accounts for approximately 15% of all breast cancer cases, with over 35,000 newly diagnosed women per year in the USA. TNBC patients are at high risk of recurrence, and neoadjuvant standard chemotherapy leads to pathologic complete response in only about 30% of patients. No targeted therapy has yet been conclusively established to improve outcome. The management of TNBC will significantly improve once mechanisms responsible for TNBC resistance to chemotherapies are identified. Here, we applied a new functional proteomic strategy to reveal which (dys)regulated phospho-signaling circuits are the effective dependencies of chemotherapy-resistant TNBC cells. The high-throughput kinase activity-mapping (HT-KAM) assay is our new screening technology to assess the catalytic activity of many kinases in parallel. HT-KAM relies on collections of biologic peptide probes that are computationally derived from PhosphoAtlas (Olow and Chen et al., Cancer Research 2016) and are physically used as combinatorial sensors to measure the activity of kinase enzymes in biologic extracts. The HT-KAM system provides access to a vast, untapped resource of meaningful measurements, whether readouts are interpreted irrespective of which enzymes phosphorylate which probes, or analyzed to convert global phospho-signatures into functional profiles of kinase activities. Kinome maps reveal how signaling networks are rewired by drug interventions in the context of different cellular backgrounds or exogenously mutated proteins/pathways, and provide insight into potentially targetable pathways. We previously successfully showed that the HT-KAM platform identifies new, actionable kinases responsible for intrinsic or acquired targeted-therapy resistance in BRAFV600E colorectal cancer cells and melanoma tumors from patients. To study TNBC, we used a 615-peptide sensor library that supports the mapping of >100 kinases and represents >900 functional kinase-substrate interactions relevant to tumor biology, and matches hundreds of druggable components of signaling circuits. We characterized the phospho-catalytic signatures of 10 TNBC cell lines, either untreated or treated with chemotherapeutic drugs (5-FU, carboplatin, doxorubicin) at IC50 concentrations. We also included a panel of 8 luminal BC cells. Based on our advanced preliminary data, we anticipate showing a comprehensive map of the oncogenic kinome of TNBC, and how it rewires its signaling network in response to chemotherapies. The most hyperactive and conserved pathways establish a priority map of strategic kinase hot spots to explore as therapeutic candidates. We find that chemotherapy-induced kinases such as SRC, AKT, CHEK, or regulating NFkB or PARP pathways can be inhibited to improve therapeutic sensitivity in TNBC. Citation Format: Jean-Philippe F. Coppe, Pan Bo, Carolien van der Borden, Nina Koemans, Changjun Wang, Denise Wolf, Christina Yau, Sietske Bakker, Marij Hartog, Miki Mori, Ana Ruiz-Saenz, Zhongzhong Chen, Aleksandra Olow, Pei Rong Evelyn Lee, Laura van 't Veer. Systematic identification of the actionable kinase dependencies of chemotherapy-resistant triple-negative breast cancer [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 956.

Background: Improper control of phosphorylation networks represents a powerful regulator and biomarker of cell dys-function leading to malignancy. Discovering which active mechanisms of disease progression can be efficiently targeted, and knowing whether kinase networks circumvent therapeutic interventions, are challenges researchers and clinicians face. Surprisingly however, measuring the phosphorylating activity of kinases, and potentially monitoring the functionality of the entire human phospho-reactome at once, remains largely unexplored. We developed a semi-high throughput assay to monitor the phospho-catalytic activity of kinase enzymes, using their biological targets as phospho-sensors. We successfully used this assay to identify the active, oncogenic phospho-signature of breast cancer cells. Methods: We first built a library of peptide sensors established from confirmed kinase substrates' phosphorylation sites. Precisely, we used computational methods to create a unique phospho-repertoire cataloguing 3,408 peptide sequences established from validated human proteins' phosphorylation sites, curated from 38 public databases. Second, we experimentally used these biologically relevant probes in multiplex assays to measure the catalytic state of kinases. Specifically, 228 peptides were developed into an ATP-consumption screen to identify the activity signatures of AKT, EGFR, MAPK, ABL and SRC family kinases. We developed analysis methods to derive phospho-signatures from semi-high throughput measurements. Finally, we validated the bio-applicability of the assay using isogenic culture model of basal-like breast cancer (HMT-3522 S1 and T4-2), and cell lines harboring EGFR/HER2-oncogenic alterations (MDA-MB-231, AU565, MCF7, T47D). Results: The differential phosphorylation activity of 25 recombinant, active kinase enzymes was successfully captured on 228 phospho-sensing peptides. In cancer cell extracts, hyper-activated AKT, SRC, EGFR, or MAPK kinases originally identified by immuno-detection were reliably and specifically detectable using the peptide-based kinase-activity assay. The phospho-sensing assay revealed the heterogeneity of kinase activity networks in breast cancer cells, and possible new drug-targeting opportunities. Conclusion: This unique strategy and resources allows to comprehensively measure the catalytic activity of a multitude of kinases at once, ultimately representing a new molecular dimension to characterize biological samples. Such new phospho-reactome profiling system suggests how chemotherapeutic interventions affect the activity of kinases and lead to reprogramming of phospho-circuits. Our efforts now concentrate on expanding this approach into a high-content, functional kinome-screening platform to map phosphorylation signatures that cause breast malignancies, therapeutic resistance, or recurrence. Citation Format: Jean-Philippe F. Coppé, Miki Mori, Evelyn Lee, Bo Pan, Aaron Boudreau, Zhongzhong Chen, Laura van 't Veer. Phospho-reactome profiling reveals the heterogenic, targetable kinase signature of breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5309. doi:10.1158/1538-7445.AM2014-5309