Motivation: Availability of large-scale genomic, epigenetic and proteomic data in complex disease... more Motivation: Availability of large-scale genomic, epigenetic and proteomic data in complex diseases makes it possible to objectively and comprehensively identify the therapeutic targets that can lead to new therapies. The Connectivity Map has been widely used to explore novel indications of existing drugs. However, the prediction accuracy of the existing methods, such as Kolmogorov-Smirnov statistic remains low. Here we present a novel high-performance drug repositioning approach that improves over the state-of-the-art methods. Results: We first designed an expression weighted cosine (EWCos) method to minimize the influence of the uninformative expression changes and then developed an ensemble approach termed ensemble of multiple drug repositioning approaches (EMUDRA) to integrate EWCos and three existing state-of-the-art methods. EMUDRA significantly outperformed individual drug repositioning methods when applied to simulated and independent evaluation datasets. We predicted using EMUDRA and experimentally validated an antibiotic rifabutin as an inhibitor of cell growth in triple negative breast cancer. EMUDRA can identify drugs that more effectively target disease gene signatures and will thus be a useful tool for identifying novel therapies for complex diseases and predicting new indications for existing drugs.
Background: The protein kinase C (PKC) family comprises distinct classes of proteins, many of whi... more Background: The protein kinase C (PKC) family comprises distinct classes of proteins, many of which are implicated in diverse cellular functions. Protein tyrosine kinase C theta isoform (PRKCQ)/PKCθ, a member of the novel PKC family, may have a distinct isoform-specific role in breast cancer. PKCθ is preferentially expressed in triple-negative breast cancer (TNBC) compared to other breast tumor subtypes. We hypothesized that PRKCQ/PKCθ critically regulates growth and survival of a subset of TNBC cells. Methods: To elucidate the role of PRKCQ/PKCθ in regulating growth and anoikis resistance, we used both gain and loss of function to modulate expression of PRKCQ. We enhanced expression of PKCθ (kinase-active or inactive) in non-transformed breast epithelial cells (MCF-10A) and assessed effects on epidermal growth factor (EGF)independent growth, anoikis, and migration. We downregulated expression of PKCθ in TNBC cells, and determined effects on in vitro and in vivo growth and survival. TNBC cells were also treated with a small molecule inhibitor to assess requirement for PKCθ kinase activity in the growth of TNBC cells. Results: PRKCQ/PKCθ can promote oncogenic phenotypes when expressed in non-transformed MCF-10A mammary epithelial cells; PRKCQ/PKCθ enhances anchorage-independent survival, growth-factor-independent proliferation, and migration. PKCθ expression promotes retinoblastoma (Rb) phosphorylation and cell-cycle progression under growth factor-deprived conditions that typically induce cell-cycle arrest of MCF-10A breast epithelial cells. Proliferation and Rb phosphorylation are dependent on PKCθ-stimulated extracellular signal-related kinase (Erk)/mitogen-activated protein kinase (MAPK) activity. Enhanced Erk/MAPK activity is dependent on the kinase activity of PKCθ, as overexpression of kinase-inactive PKCθ does not stimulate Erk/MAPK or Rb phosphorylation or promote growth-factor-independent proliferation. Downregulation of PRKCQ/PKCθ in TNBC cells enhances anoikis, inhibits growth in 3-D Matrigel TM cultures, and impairs triple-negative tumor xenograft growth. AEB071, an inhibitor of PKCθ kinase activity, also inhibits growth and invasive branching of TNBC cells in 3-D cultures, further supporting a role for PKCθ kinase activity in triple-negative cancer cell growth. Conclusions: Enhanced PRKCQ/PKCθ expression can promote growth-factor-independent growth, anoikis resistance, and migration. PRKCQ critically regulates growth and survival of a subset of TNBC. Inhibition of PKCθ kinase activity may be an attractive therapeutic approach for TNBC, a subtype in need of improved targeted therapies.
Aminoacyl tRNA synthetases (ARSs) are a class of enzymes with well-conserved housekeeping functio... more Aminoacyl tRNA synthetases (ARSs) are a class of enzymes with well-conserved housekeeping functions in cellular translation. Recent evidence suggests that ARS genes may participate in a wide array of cellular processes, and may contribute to the pathology of autoimmune disease, cancer, and other diseases. Several studies have suggested a role for the glutamyl prolyl tRNA synthetase (EPRS) in breast cancers, although none has identified any underlying mechanism about how EPRS contributes to carcinogenesis. In this study, we identified EPRS as upregulated in estrogen receptor positive (ER+) human breast tumors in the TCGA and METABRIC cohorts, with copy number gains in nearly 50% of samples in both datasets. EPRS expression is associated with reduced overall survival in patients with ER+ tumors in TCGA and METABRIC datasets. EPRS expression was also associated with reduced distant relapse-free survival in patients treated with adjuvant tamoxifen monotherapy for five years, and EPRS-correlated genes were highly enriched for genes predictive of a poor response to tamoxifen. We demonstrated the necessity of EPRS for proliferation of tamoxifen-resistant ER+ breast cancer, but not ER-breast cancer cells. Transcriptomic profiling showed that EPRS regulated cell cycle and estrogen response genes. Finally, we constructed a causal gene network based on over 2500 ER+ breast tumor samples to build up an EPRS-estrogen signaling pathway. EPRS and its regulated estrogenic gene network may offer a promising alternative approach to target ER+ breast cancers that are refractory to current anti-estrogens.
Background: Proteins that are required for anchorage-independent survival of tumor cells represen... more Background: Proteins that are required for anchorage-independent survival of tumor cells represent attractive targets for therapeutic intervention since this property is believed to be critical for survival of tumor cells displaced from their natural niches. Anchorage-independent survival is induced by growth factor receptor hyperactivation in many cell types. We aimed to identify molecules that critically regulate IGF-1-induced anchorage-independent survival. Methods and Results: We conducted a high-throughput siRNA screen and identified PTK6 as a critical component of IGF-1 receptor (IGF-1R)-induced anchorage-independent survival of mammary epithelial cells. PTK6 downregulation induces apoptosis of breast and ovarian cancer cells deprived of matrix attachment, whereas its overexpression enhances survival. Reverse-phase protein arrays and subsequent analyses revealed that PTK6 forms a complex with IGF-1R and the adaptor protein IRS-1, and modulates anchorage-independent survival by regulating IGF-1R expression and phosphorylation. PTK6 is highly expressed not only in the previously reported Her2 + breast cancer subtype, but also in high grade ER + , Luminal B tumors and high expression is associated with adverse outcomes. Conclusions: These findings highlight PTK6 as a critical regulator of anchorage-independent survival of breast and ovarian tumor cells via modulation of IGF-1 receptor signaling, thus supporting PTK6 as a potential therapeutic target for multiple tumor types. The combined genomic and proteomic approaches in this report provide an effective strategy for identifying oncogenes and their mechanism of action.
Background/Rationale: While some patients with triple negative breast cancer (TNBC) achieve long-... more Background/Rationale: While some patients with triple negative breast cancer (TNBC) achieve long-term remission with standard-of-care chemotherapy, many have cancers that are chemotherapy resistant, putting them at risk for metastatic recurrence. There is also a lack of targeted therapies for TNBC, highlighting the need for novel therapeutic strategies for this subtype. PRKCQ, a member of the novel protein kinase C family, is preferentially expressed in TNBC compared to other breast cancer subtypes and we previously reported that PRKCQ expression is sufficient to promote oncogenic activities (growth-factor independent growth, anoikis resistance and migration). In addition, PRKCQ suppression inhibits growth of TNBC tumor xenografts. We sought to determine if PRKCQ expression modulation impacts sensitivity of triple negative breast cancer cells to standard of care chemotherapy and whether PRKCQ inhibition could be a strategy to enhance chemosensitivity of drug-resistant TNBC. Methods: We determined the effects of modulating PRKCQ expression, using PRKCQ cDNA or shRNA vectors, on sensitivity of TNBC cells to the apoptotic effects of standard-of-care chemotherapy, including those cancers that are relatively chemotherapy resistant at baseline. We also determined the mechanisms by which PRKCQ regulates sensitivity to chemotherapy. Results: Increased PRKCQ expression in non-transformed MCF-10A breast epithelial cells promotes resistance to the apoptosis-inducing effects of Doxorubicin or Paclitaxel treatment. These effects are dependent on PRKCQ kinase activity as a catalytically inactive PRKCQ failed to promote resistance. Downregulation of PRKCQ or inhibition of its kinase activity enhanced sensitivity of TNBC cells to chemotherapy. PRKCQ impacts chemotherapy sensitivity of TNBC by regulating epithelial-mesenchymal transition (EMT) and expression of Bim, a pro-apoptotic Bcl2 family protein. Conclusions. PRKCQ promotes resistance of TNBC to standard of care chemotherapies by promoting EMT and suppressing pro-apoptotic Bim. Inhibiting PRKCQ expression or activity sensitizes TNBC cells to chemotherapy and could be an effective strategy to overcome chemotherapy resistance of a subset of triple negative breast cancers, thereby improving patient outcomes. Citation Format: Hanna Yoko Irie, Jessica H. Byerly, Elisa R. Port. Inhibition of PRKCQ enhances chemosensitivity of triple negative breast cancer by regulating EMT and Bim [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 P3-06-14.
Background/Rationale : PRKCQ, a member of the novel protein kinase C family, was identified in a ... more Background/Rationale : PRKCQ, a member of the novel protein kinase C family, was identified in a functional genomic screen for regulators of anoikis resistance/anchorage-independent survival (Irie et al., 2010). Interestingly, it is preferentially expressed in the triple negative/basal subtype of breast tumors compared to Luminal or Her2+ tumors. We sought to determine the functional role of PRKCQ in triple negative breast cancer and evaluate PRKCQ as a candidate therapeutic target for this subtype. Materials and Methods . Consistent with its expression in triple negative patient breast tumors, PRKCQ is also highly expressed in several triple negative breast cancer cell lines. We utilized both gain- and loss-of-function approaches in these cell lines to determine the requirement for PRKCQ in oncogenic growth and survival using in vitro and in vivo models. Results . Isoform-specific downregulation of PRKCQ using shRNA vectors severely impaired growth of triple negative breast cancer cells in 2D monolayer and 3D Matrigel cultures. In 3D cultures, PRKCQ downregulation not only inhibited growth, but impaired the formation of invasive branching. PRKCQ downregulation also inhibited the growth of MDA231 primary tumor xenografts. All of these data support a requirement for PRKCQ expression in triple negative breast cancer cell growth. To determine if PRKCQ is sufficient to drive oncogenic phenotypes, we overexpressed PRKCQ in a non-transformed immortalized breast epithelial cell line, MCF-10A. PRKCQ expression conferred EGF-independent growth, migration and anoikis resistance. In PRKCQ-expressing MCF-10A cells, EGFR phosphorylation and activation were preserved in the absence of exogenous EGF ligand addition. We are currently elucidating the mechanisms responsible for PRKCQ-mediated, sustained activation of EGFR. Conclusions . PRKCQ is critically required for growth of triple negative breast cancer cells. Increased expression of PRKCQ is sufficient to drive oncogenic, growth factor-independent growth, survival and migration. Interestingly, PRKCQ could play a dual role in the development of triple negative breast cancer, as it may also function in the immune microenvironment to support the growth of these tumors. Therefore, PRKCQ is an attractive candidate therapeutic target for patients with triple negative breast cancer. Citation Format: Hanna Y Irie, Gwyneth Halstead-Nussloch, Koichi Ito. PRKCQ, a novel protein kinase C preferentially expressed in triple negative breast cancer, drives oncogenic growth, survival and migration [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 P4-05-10.
PURPOSE/OBJECTIVES: A growing body of evidence demonstrates that patient-derived xenografts (PDXs... more PURPOSE/OBJECTIVES: A growing body of evidence demonstrates that patient-derived xenografts (PDXs) represent living tumor models that accurately reflect the biology of the primary patient tumor. More importantly, we have previously shown that PDX models show responses to therapeutic agents that are concordant with patient clinical response and can be used to direct personalized cancer treatments (Stebbing, 2014). Here we report the ability of PDX models to predict for patient response to drug treatment in a cohort of breast cancer patients. MATERIALS/METHODS: Tumors were resected from patients with either primary or metastatic breast cancer and implanted into immunodeficient mice to establish PDX models. Successfully engrafted PDX models were expanded and randomized for drug sensitivity testing. Tumor growth inhibition and tumor regression were captured and results were correlated with a patient’s clinical response. In some cases, PDX results were used to personalize cancer treatment and some patients used PDX-directed treatments over multiple lines of therapy. RESULTS: A total of 42 tumors from 40 patients were implanted resulting in 21 successfully engrafted PDX models (50% engraftment rate). Notably, engraftment rates were much higher for patients with triple negative breast cancer (TNBC) and resulted in 7 successful PDX models from 8 TNBC patients (87.5% engraftment rate). Drug sensitivity testing was offered to patients with established PDX models. Drugs and drug combinations tested included standard and nonstandard chemotherapy as well as biologics. At that time of this publication, 4 patients (3 TNBC and 1 HER2+) with completed drug sensitivity tests also had clinical data available resulting in 7 clinical correlations; 4 retrospective and 3 prospective. In all 7 cases, the PDX model accurately predicted patient clinical response demonstrating an accuracy of 100%. Five of the drug tests predicted drug sensitivity and 2 tests predicted resistance, indicating the potential of the PDX platform to predict for both sensitivity and resistance to therapy. The 3 prospective correlations resulted in concordant clinical benefit in 2 patients for duration greater than 6 months each. CONCLUSIONS: These data support the use of the personalized PDX model as a platform for therapeutic decision making that can guide treatment for patients with breast cancer. A prospective clinical trial in TNBC is currently underway. Citation Format: Lisa Stow, Amanda Katz, Hanna Irie, Elisa Port, Justin Stebbing, Daniel Ciznadija, Angela Davies, Keren Paz. Patient-derived xenografts accurately predict patient response in breast cancer patients [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 P3-06-31.
Background: Protein kinase C theta, (PRKCQ/PKCθ) is a serine/threonine kinase that is highly expr... more Background: Protein kinase C theta, (PRKCQ/PKCθ) is a serine/threonine kinase that is highly expressed in a subset of triple-negative breast cancers (TNBC) and promotes their growth, anoikis resistance, epithelial-mesenchymal transition (EMT), and invasion. Here, we show that PRKCQ regulates the sensitivity of TNBC cells to apoptosis triggered by standard-of-care chemotherapy by regulating levels of pro-apoptotic Bim. Methods: To determine the effects of PRKCQ expression on chemotherapy-induced apoptosis, shRNA and cDNA vectors were used to modulate the PRKCQ expression in MCF-10A breast epithelial cells or triple-negative breast cancer cells (MDA-MB231Luc, HCC1806). A novel PRKCQ small-molecule inhibitor, 17k, was used to inhibit kinase activity. Viability and apoptosis of cells treated with PRKCQ cDNA/shRNA/inhibitor +/-chemotherapy were measured. Expression levels of Bcl2 family members were assessed. Results: Enhanced expression of PRKCQ is sufficient to suppress apoptosis triggered by paclitaxel or doxorubicin treatment. Downregulation of PRKCQ also enhanced the apoptosis of chemotherapy-treated TNBC cells. Regulation of chemotherapy sensitivity by PRKCQ mechanistically occurs via regulation of levels of Bim, a pro-apoptotic Bcl2 family member; suppression of Bim prevents the enhanced apoptosis observed with combined PRKCQ downregulation and chemotherapy treatment. Regulation of Bim and chemotherapy sensitivity is significantly dependent on PRKCQ kinase activity; overexpression of a catalytically inactive PRKCQ does not suppress Bim or chemotherapy-associated apoptosis. Furthermore, PRKCQ kinase inhibitor treatment suppressed growth, increased anoikis and Bim expression, and enhanced apoptosis of chemotherapy-treated TNBC cells, phenocopying the effects of PRKCQ downregulation. Conclusions: These studies support PRKCQ inhibition as an attractive therapeutic strategy and complement to chemotherapy to inhibit the growth and survival of TNBC cells.
Introduction: Protein tyrosine kinase 6 (PTK6) is a non-receptor tyrosine kinase that is highly e... more Introduction: Protein tyrosine kinase 6 (PTK6) is a non-receptor tyrosine kinase that is highly expressed in Human Epidermal Growth Factor 2 + (Her2 +) breast cancers. Overexpression of PTK6 enhances anchorage-independent survival, proliferation, and migration of breast cancer cells. We hypothesized that PTK6 inhibition is an effective strategy to inhibit growth and survival of Her2 + breast cancer cells, including those that are relatively resistant to Lapatinib, a targeted therapy for Her2 + breast cancer, either intrinsically or acquired after continuous drug exposure. Methods: To determine the effects of PTK6 inhibition on Lapatinib-resistant Her2 + breast cancer cell lines (UACC893R1 and MDA-MB-453), we used short hairpin ribonucleic acid (shRNA) vectors to downregulate PTK6 expression. We determined the effects of PTK6 downregulation on growth and survival in vitro and in vivo, as well as the mechanisms responsible for these effects. Results: Lapatinib treatment of "sensitive" Her2 + cells induces apoptotic cell death and enhances transcript and protein levels of Bim, a pro-apoptotic Bcl2 family member. In contrast, treatment of relatively "resistant" Her2 + cells fails to induce Bim or enhance levels of cleaved, poly-ADP ribose polymerase (PARP). Downregulation of PTK6 expression in these "resistant" cells enhances Bim expression, resulting in apoptotic cell death. PTK6 downregulation impairs growth of these cells in in vitro 3-D Matrigel TM cultures, and also inhibits growth of Her2 + primary tumor xenografts. Bim expression is critical for apoptosis induced by PTK6 downregulation, as co-expression of Bim shRNA rescued these cells from PTK6 shRNA-induced death. The regulation of Bim by PTK6 is not via changes in Erk/MAPK or Akt signaling, two pathways known to regulate Bim expression. Rather, PTK6 downregulation activates p38, and pharmacological inhibition of p38 activity prevents PTK6 shRNA-induced Bim expression and partially rescues cells from apoptosis. Conclusions: PTK6 downregulation induces apoptosis of Lapatinib-resistant Her2 + breast cancer cells by enhancing Bim expression via p38 activation. As Bim expression is a critical biomarker for response to many targeted therapies, PTK6 inhibition may offer a therapeutic approach to treating patients with Her2 targeted therapy-resistant breast cancers.
Background/Rationale: Sensitivity to chemotherapy consistently remains a strong predictor of long... more Background/Rationale: Sensitivity to chemotherapy consistently remains a strong predictor of long term outcomes and survival for patients diagnosed with triple negative breast cancer (TNBC). Patients who do not achieve a complete pathological response to pre-operative, neoadjuvant chemotherapy are at increased risk for metastatic recurrence. Clinical trials with targeted therapies and immunotherapies aim to reduce this risk of recurrence for this patient population. As part of our ongoing prospective study of patients with TNBC that involves serial blood collections and tissue collections (pre-treatment biopsy and post-neoadjuvant surgical specimen) from the time of initial diagnosis, we are particularly focused on those patients with residual disease following neoadjuvant treatment. Comprehensive tissue and cell-free DNA (cfDNA)/circulating tumor cell (CTC) profiling of these patients could lead to insights into mechanisms of chemotherapy resistance and new treatment strategies to prevent recurrences. In addition to genomic profiling, we have analyzed PD-L1 expression on tissue and CTC’s which may contribute to improve targeted utilization of immunotherapies for patients with early stage, high-risk TNBC. Methods: Patients diagnosed with TNBC (stage 1-3) are consented for this prospective study. Serial collections of blood are obtained at time of initial diagnosis, following neoadjuvant chemotherapy or upfront surgery and at 6 month intervals following completion of all active therapy. cfDNA/CTC are isolated using Cynvenio’s Liquid Biopsy platform and sequenced on a rolling basis with Oncomine V3 panel. Tissue from initial biopsy and surgical resection are also collected and sequenced. PD-L1 staining of breast tumor tissue and CTC is performed using antibody SP-142 and atezolizumab, respectively. Clinical outcomes (response to chemotherapy and recurrence data) are also recorded. Results: 30 patients are currently being followed. Of these 24 patients were treated with neoadjuvant chemotherapy and 10/24 (42%) had a pathological complete response (pCR). For the patients treated with neoadjuvant chemotherapy whose pre-treatment samples have been sequenced, 3/6 (50%) of patients who did not achieve a pCR had pre-treatment detectable mutations in cfDNA/CTC in contrast to 3/9 (33%) patients who achieved a pCR. Furthermore, all 6 patients who had residual disease had at least one blood collection with detectable cfDNA/CTC mutations following completion of all active breast cancer therapy. For the five patients with post-neoadjuvant residual disease whose surgical specimens have been stained for PD-L1 expression, 4/5 (80%) are PD-L1 positive (>1%) either in the tumor or infiltrating leukocyte population. PD-L1 positive circulating CTC’s were also detected in 1 of these patients with PD-L1 positive residual disease thus far. Conclusions: Prospective serial analysis of cfDNA/CTC may identify patients who are at higher risk for incomplete response to neoadjuvant therapy or metastatic recurrence. PD-L1 staining of post-neoadjuvant residual cancer and/or CTC’s may help identify high risk patients most likely to benefit from adjuvant immunotherapy. Citation Format: Hanna Yoko Irie, Paul Schmidt, Elisa Port, Natalie Berger, Paula Klein, Yayoi Kinoshita, Alan Soto, Kereeti Pisapati, Ronald Couri, Olivia Kolodka, Hanane Arib, Robert Sebra, Michael J Donovan. Prospective genomic and PD-L1 profiling of patients with residual triple negative breast cancer after neoadjuvant chemotherapy [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 P5-01-09.
e24108Background: Patients with early stage triple negative breast cancer (TNBC) are treated with... more e24108Background: Patients with early stage triple negative breast cancer (TNBC) are treated with multimodality therapy (chemotherapy, surgery, radiation). Cell-free DNA (cfDNA) and circulating tum...
e23070 Background: Serial liquid biopsy assessment provides a unique platform for detecting exist... more e23070 Background: Serial liquid biopsy assessment provides a unique platform for detecting existing and / or emergent resistance mutations; it may be particularly beneficial when patients begin to progress on otherwise effective therapy. We aimed to determine the utility of such an approach for detection of tumor genetic alterations at multiple points during the clinical course of patients diagnosed with breast cancer. Methods: Twenty patients diagnosed with stage I-IV breast cancer (50% with triple negative disease) receiving treatment at the Dubin Center of Mount Sinai were consented for serial CTC/cfDNA collections between October 2015 and November 2016. Circulating tumor cell (CTC)/cell-free DNA (cfDNA) were isolated using Cynvenio’s Liquid Biopsy platform and sequenced utilizing the Hotspot/Oncomine panels. DNA from corresponding patient tumors, when available, was also sequenced. Results: 25% of patients had at least one known pathogenic mutation detected in either cfDNA or CTC DNA in at least one collection; all patients had stage IV disease at collection. Pathogenic mutations detected were in p53 (15%), PIK3CA (10%) and Smad4 (5%). For those patients with available tumor tissue, the same pathogenic mutation was detected in the primary tumor. Mutations were more often detected in cfDNA rather than CTC DNA. Finally, known pathogenic mutations were more consistently detected in serial collections with clinical disease progression and resistance to treatment. Conclusions: Pathogenic mutations were identified in 25% of patients, more frequently in cfDNA and not in every collected sample, supporting serial collection studies to monitor response. Presence of same pathogenic mutations in the patient’s primary tumor suggest a role for surveillance in early stage, as well as advanced disease.
e12594Background: Obesity and weight gain are significant concerns for breast cancer survivors. O... more e12594Background: Obesity and weight gain are significant concerns for breast cancer survivors. Obesity at diagnosis of breast cancer is an established negative prognostic factor and post-diagnosis...
Background: Niraparib is a selective poly(ADP-ribose) polymerase 1/2 inhibitor that has demonstra... more Background: Niraparib is a selective poly(ADP-ribose) polymerase 1/2 inhibitor that has demonstrated antitumor activity in advanced triple-negative breast cancer (TNBC) in combination with a programmed cell death 1 inhibitor, with the greatest clinical activity seen in tumors with breast cancer susceptibility gene (BRCA) mutations. Pharmacologically, niraparib has demonstrated a wide volume of distribution and high cell membrane permeability. In breast and ovarian cancer xenograft mouse models, niraparib achieved tumor exposures that were 3.3 times greater than plasma exposure. The objective of this study is to evaluate the antitumor activity of single-agent niraparib in the neoadjuvant treatment of patients with localized, human epidermal growth factor receptor 2 (HER2)-negative, BRCA-mutated breast cancer. The relative concentration of niraparib in tumor versus plasma was also assessed. Methods: Eligible patients were ≥18 years old, with HER2-negative, BRCA-mutated (germline or so...
108600, a novel CK2/DYRK1/TNIK inhibitor, targets and inhibits cancer stem cells (CSC) in triple ... more 108600, a novel CK2/DYRK1/TNIK inhibitor, targets and inhibits cancer stem cells (CSC) in triple negative breast cancer (TNBC), inhibiting tumor growth and metastases in patient-derived xenograft models. CSC’s have been shown to promote immune evasion of several types of cancer. Specifically, over-expression of CK2 has been shown to promote intratumoral recruitment of myeloid derived suppressor cells. We investigated the effects of 108600 treatment on the immune microenvironment of triple negative breast cancer since targeting CSC’s could promote favorable anti-tumor immune responses and mechanistically contribute to tumor growth inhibition. Methods:C57BL/6 mice bearing murine triple negative E0771 tumors were generated by orthotopic injection and treated either with vehicle control or 108600 for 5 days. Tumor growth was assessed by daily caliper measurement All tumors were recovered at endpoint, and processed for RNA sequencing, flow cytometry or Western blot analysis. Results:1086...
Background/Rational: Patients with triple negative breast cancers (TNBC) have limited therapeutic... more Background/Rational: Patients with triple negative breast cancers (TNBC) have limited therapeutic options beyond conventional chemotherapy. Unfortunately, high-risk for metastatic recurrence and chemotherapy resistant diseases cause the worst 5-year survival rate in patients with TNBC, which have been significant clinical challenges. Novel therapeutic targets or strategies to combat metastasis and chemotherapy resistance are necessary to improve quality of life and outcomes for patients with high risk TNBC. Epithelial-to-mesenchymal transition (EMT) and anoikis resistance are processes recognized as contributing to enhanced metastatic potential and treatment resistance. A subset of TNBC exhibits mesenchymal gene signatures and phenotypes that may be associated with high metastatic recurrence, chemotherapy resistance and immunosuppression. In a functional genomic screen, we identified several candidates as novel regulators of EMT and anoikis sensitivity of TNBC cells. We have focused...
TPS1103Background: Overexpression or amplification of HER2 occurs in approximately 15 – 20% of pa... more TPS1103Background: Overexpression or amplification of HER2 occurs in approximately 15 – 20% of patients and about half of these tumors are hormone receptor (HR) positive. Studies suggest that this 10% of all breast cancer cases may derive less benefit from endocrine therapy than those with HR+ disease without HER2 overexpression. The use of aromatase inhibitors in the metastatic setting is well established while significant improvement in overall survival has been established with the use of trastuzumab or pertuzumab in HER2-overexpressing tumors. To date, no studies have examined the combination of endocrine therapy, palbociclib, and dual HER2 therapy with pertuzumab and trastuzumab in this patient population. Trial Design: Multicenter, Phase I/II Trial of Anastrozole, Palbociclib, Trastuzumab and Pertuzumab in HR-positive, Her2-positive Metastatic Breast Cancer. Eligibility Criteria: Stage IV HR+, HER2+ breast cancer patients. Specific Aims: Phase I: To determine the maximum dose tolerated of palbocicli...
e14307 Background: Mutation-derived tumor antigens (MTAs) arise as a direct result of somatic var... more e14307 Background: Mutation-derived tumor antigens (MTAs) arise as a direct result of somatic variations that occur during carcinogenesis and can be characterized via genetic sequencing and used to identify MTAs. We developed a platform for a fully-personalized MTA-based vaccine in the adjuvant treatment of solid and hematological malignancies. Methods: This is a single-arm, open label, proof-of-concept phase I study designed to test the safety and immunogenicity of Personalized Genomic Vaccine 001 (PGV001) that targets up to 10 predicted personal tumor neoantigens based on patient’s HLA profile (ClinicalTrials.gov: NCT02721043). Results: Patients who completed vaccination with PGV001_002 (head and neck squamous cell cancer) received 10 doses of vaccine comprising 10 long peptides (LP) combined with poly-ICLC (toll-like receptor-3 agonist) intradermally. Vaccine-induced T-cell responses were determined at weeks 0 and 27 (before and after treatment, respectively), ex vivo by interfer...
TPS1109 Background: Triple negative breast cancer (TNBC) is an aggressive disease with unmet clin... more TPS1109 Background: Triple negative breast cancer (TNBC) is an aggressive disease with unmet clinical needs. Women with TNBC tend to be younger and demonstrate early recurrence, higher histological grade, higher rate of visceral metastasis and increased mortality rates when compared to hormone positive breast cancer. Prognosis for metastatic TNBC is especially poor. Due to lack of targeted therapies, there is no standard treatment of choice for triple negative breast cancer and chemotherapy remains the accepted standard. Many chemotherapeutic agents have been reported to have clinical activity either as single agent or in combination. Seventy percent of breast cancers with BRCA-1 germline mutations are triple negative, which suggests a shared carcinogenic pathway between them. In preoperative and metastatic settings, both TNBC and BRCA-1 associated breast cancers are particularly sensitive to DNA cross-linking agents such as platinum compounds due to defective DNA repair by homologo...
Motivation: Availability of large-scale genomic, epigenetic and proteomic data in complex disease... more Motivation: Availability of large-scale genomic, epigenetic and proteomic data in complex diseases makes it possible to objectively and comprehensively identify the therapeutic targets that can lead to new therapies. The Connectivity Map has been widely used to explore novel indications of existing drugs. However, the prediction accuracy of the existing methods, such as Kolmogorov-Smirnov statistic remains low. Here we present a novel high-performance drug repositioning approach that improves over the state-of-the-art methods. Results: We first designed an expression weighted cosine (EWCos) method to minimize the influence of the uninformative expression changes and then developed an ensemble approach termed ensemble of multiple drug repositioning approaches (EMUDRA) to integrate EWCos and three existing state-of-the-art methods. EMUDRA significantly outperformed individual drug repositioning methods when applied to simulated and independent evaluation datasets. We predicted using EMUDRA and experimentally validated an antibiotic rifabutin as an inhibitor of cell growth in triple negative breast cancer. EMUDRA can identify drugs that more effectively target disease gene signatures and will thus be a useful tool for identifying novel therapies for complex diseases and predicting new indications for existing drugs.
Background: The protein kinase C (PKC) family comprises distinct classes of proteins, many of whi... more Background: The protein kinase C (PKC) family comprises distinct classes of proteins, many of which are implicated in diverse cellular functions. Protein tyrosine kinase C theta isoform (PRKCQ)/PKCθ, a member of the novel PKC family, may have a distinct isoform-specific role in breast cancer. PKCθ is preferentially expressed in triple-negative breast cancer (TNBC) compared to other breast tumor subtypes. We hypothesized that PRKCQ/PKCθ critically regulates growth and survival of a subset of TNBC cells. Methods: To elucidate the role of PRKCQ/PKCθ in regulating growth and anoikis resistance, we used both gain and loss of function to modulate expression of PRKCQ. We enhanced expression of PKCθ (kinase-active or inactive) in non-transformed breast epithelial cells (MCF-10A) and assessed effects on epidermal growth factor (EGF)independent growth, anoikis, and migration. We downregulated expression of PKCθ in TNBC cells, and determined effects on in vitro and in vivo growth and survival. TNBC cells were also treated with a small molecule inhibitor to assess requirement for PKCθ kinase activity in the growth of TNBC cells. Results: PRKCQ/PKCθ can promote oncogenic phenotypes when expressed in non-transformed MCF-10A mammary epithelial cells; PRKCQ/PKCθ enhances anchorage-independent survival, growth-factor-independent proliferation, and migration. PKCθ expression promotes retinoblastoma (Rb) phosphorylation and cell-cycle progression under growth factor-deprived conditions that typically induce cell-cycle arrest of MCF-10A breast epithelial cells. Proliferation and Rb phosphorylation are dependent on PKCθ-stimulated extracellular signal-related kinase (Erk)/mitogen-activated protein kinase (MAPK) activity. Enhanced Erk/MAPK activity is dependent on the kinase activity of PKCθ, as overexpression of kinase-inactive PKCθ does not stimulate Erk/MAPK or Rb phosphorylation or promote growth-factor-independent proliferation. Downregulation of PRKCQ/PKCθ in TNBC cells enhances anoikis, inhibits growth in 3-D Matrigel TM cultures, and impairs triple-negative tumor xenograft growth. AEB071, an inhibitor of PKCθ kinase activity, also inhibits growth and invasive branching of TNBC cells in 3-D cultures, further supporting a role for PKCθ kinase activity in triple-negative cancer cell growth. Conclusions: Enhanced PRKCQ/PKCθ expression can promote growth-factor-independent growth, anoikis resistance, and migration. PRKCQ critically regulates growth and survival of a subset of TNBC. Inhibition of PKCθ kinase activity may be an attractive therapeutic approach for TNBC, a subtype in need of improved targeted therapies.
Aminoacyl tRNA synthetases (ARSs) are a class of enzymes with well-conserved housekeeping functio... more Aminoacyl tRNA synthetases (ARSs) are a class of enzymes with well-conserved housekeeping functions in cellular translation. Recent evidence suggests that ARS genes may participate in a wide array of cellular processes, and may contribute to the pathology of autoimmune disease, cancer, and other diseases. Several studies have suggested a role for the glutamyl prolyl tRNA synthetase (EPRS) in breast cancers, although none has identified any underlying mechanism about how EPRS contributes to carcinogenesis. In this study, we identified EPRS as upregulated in estrogen receptor positive (ER+) human breast tumors in the TCGA and METABRIC cohorts, with copy number gains in nearly 50% of samples in both datasets. EPRS expression is associated with reduced overall survival in patients with ER+ tumors in TCGA and METABRIC datasets. EPRS expression was also associated with reduced distant relapse-free survival in patients treated with adjuvant tamoxifen monotherapy for five years, and EPRS-correlated genes were highly enriched for genes predictive of a poor response to tamoxifen. We demonstrated the necessity of EPRS for proliferation of tamoxifen-resistant ER+ breast cancer, but not ER-breast cancer cells. Transcriptomic profiling showed that EPRS regulated cell cycle and estrogen response genes. Finally, we constructed a causal gene network based on over 2500 ER+ breast tumor samples to build up an EPRS-estrogen signaling pathway. EPRS and its regulated estrogenic gene network may offer a promising alternative approach to target ER+ breast cancers that are refractory to current anti-estrogens.
Background: Proteins that are required for anchorage-independent survival of tumor cells represen... more Background: Proteins that are required for anchorage-independent survival of tumor cells represent attractive targets for therapeutic intervention since this property is believed to be critical for survival of tumor cells displaced from their natural niches. Anchorage-independent survival is induced by growth factor receptor hyperactivation in many cell types. We aimed to identify molecules that critically regulate IGF-1-induced anchorage-independent survival. Methods and Results: We conducted a high-throughput siRNA screen and identified PTK6 as a critical component of IGF-1 receptor (IGF-1R)-induced anchorage-independent survival of mammary epithelial cells. PTK6 downregulation induces apoptosis of breast and ovarian cancer cells deprived of matrix attachment, whereas its overexpression enhances survival. Reverse-phase protein arrays and subsequent analyses revealed that PTK6 forms a complex with IGF-1R and the adaptor protein IRS-1, and modulates anchorage-independent survival by regulating IGF-1R expression and phosphorylation. PTK6 is highly expressed not only in the previously reported Her2 + breast cancer subtype, but also in high grade ER + , Luminal B tumors and high expression is associated with adverse outcomes. Conclusions: These findings highlight PTK6 as a critical regulator of anchorage-independent survival of breast and ovarian tumor cells via modulation of IGF-1 receptor signaling, thus supporting PTK6 as a potential therapeutic target for multiple tumor types. The combined genomic and proteomic approaches in this report provide an effective strategy for identifying oncogenes and their mechanism of action.
Background/Rationale: While some patients with triple negative breast cancer (TNBC) achieve long-... more Background/Rationale: While some patients with triple negative breast cancer (TNBC) achieve long-term remission with standard-of-care chemotherapy, many have cancers that are chemotherapy resistant, putting them at risk for metastatic recurrence. There is also a lack of targeted therapies for TNBC, highlighting the need for novel therapeutic strategies for this subtype. PRKCQ, a member of the novel protein kinase C family, is preferentially expressed in TNBC compared to other breast cancer subtypes and we previously reported that PRKCQ expression is sufficient to promote oncogenic activities (growth-factor independent growth, anoikis resistance and migration). In addition, PRKCQ suppression inhibits growth of TNBC tumor xenografts. We sought to determine if PRKCQ expression modulation impacts sensitivity of triple negative breast cancer cells to standard of care chemotherapy and whether PRKCQ inhibition could be a strategy to enhance chemosensitivity of drug-resistant TNBC. Methods: We determined the effects of modulating PRKCQ expression, using PRKCQ cDNA or shRNA vectors, on sensitivity of TNBC cells to the apoptotic effects of standard-of-care chemotherapy, including those cancers that are relatively chemotherapy resistant at baseline. We also determined the mechanisms by which PRKCQ regulates sensitivity to chemotherapy. Results: Increased PRKCQ expression in non-transformed MCF-10A breast epithelial cells promotes resistance to the apoptosis-inducing effects of Doxorubicin or Paclitaxel treatment. These effects are dependent on PRKCQ kinase activity as a catalytically inactive PRKCQ failed to promote resistance. Downregulation of PRKCQ or inhibition of its kinase activity enhanced sensitivity of TNBC cells to chemotherapy. PRKCQ impacts chemotherapy sensitivity of TNBC by regulating epithelial-mesenchymal transition (EMT) and expression of Bim, a pro-apoptotic Bcl2 family protein. Conclusions. PRKCQ promotes resistance of TNBC to standard of care chemotherapies by promoting EMT and suppressing pro-apoptotic Bim. Inhibiting PRKCQ expression or activity sensitizes TNBC cells to chemotherapy and could be an effective strategy to overcome chemotherapy resistance of a subset of triple negative breast cancers, thereby improving patient outcomes. Citation Format: Hanna Yoko Irie, Jessica H. Byerly, Elisa R. Port. Inhibition of PRKCQ enhances chemosensitivity of triple negative breast cancer by regulating EMT and Bim [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 P3-06-14.
Background/Rationale : PRKCQ, a member of the novel protein kinase C family, was identified in a ... more Background/Rationale : PRKCQ, a member of the novel protein kinase C family, was identified in a functional genomic screen for regulators of anoikis resistance/anchorage-independent survival (Irie et al., 2010). Interestingly, it is preferentially expressed in the triple negative/basal subtype of breast tumors compared to Luminal or Her2+ tumors. We sought to determine the functional role of PRKCQ in triple negative breast cancer and evaluate PRKCQ as a candidate therapeutic target for this subtype. Materials and Methods . Consistent with its expression in triple negative patient breast tumors, PRKCQ is also highly expressed in several triple negative breast cancer cell lines. We utilized both gain- and loss-of-function approaches in these cell lines to determine the requirement for PRKCQ in oncogenic growth and survival using in vitro and in vivo models. Results . Isoform-specific downregulation of PRKCQ using shRNA vectors severely impaired growth of triple negative breast cancer cells in 2D monolayer and 3D Matrigel cultures. In 3D cultures, PRKCQ downregulation not only inhibited growth, but impaired the formation of invasive branching. PRKCQ downregulation also inhibited the growth of MDA231 primary tumor xenografts. All of these data support a requirement for PRKCQ expression in triple negative breast cancer cell growth. To determine if PRKCQ is sufficient to drive oncogenic phenotypes, we overexpressed PRKCQ in a non-transformed immortalized breast epithelial cell line, MCF-10A. PRKCQ expression conferred EGF-independent growth, migration and anoikis resistance. In PRKCQ-expressing MCF-10A cells, EGFR phosphorylation and activation were preserved in the absence of exogenous EGF ligand addition. We are currently elucidating the mechanisms responsible for PRKCQ-mediated, sustained activation of EGFR. Conclusions . PRKCQ is critically required for growth of triple negative breast cancer cells. Increased expression of PRKCQ is sufficient to drive oncogenic, growth factor-independent growth, survival and migration. Interestingly, PRKCQ could play a dual role in the development of triple negative breast cancer, as it may also function in the immune microenvironment to support the growth of these tumors. Therefore, PRKCQ is an attractive candidate therapeutic target for patients with triple negative breast cancer. Citation Format: Hanna Y Irie, Gwyneth Halstead-Nussloch, Koichi Ito. PRKCQ, a novel protein kinase C preferentially expressed in triple negative breast cancer, drives oncogenic growth, survival and migration [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 P4-05-10.
PURPOSE/OBJECTIVES: A growing body of evidence demonstrates that patient-derived xenografts (PDXs... more PURPOSE/OBJECTIVES: A growing body of evidence demonstrates that patient-derived xenografts (PDXs) represent living tumor models that accurately reflect the biology of the primary patient tumor. More importantly, we have previously shown that PDX models show responses to therapeutic agents that are concordant with patient clinical response and can be used to direct personalized cancer treatments (Stebbing, 2014). Here we report the ability of PDX models to predict for patient response to drug treatment in a cohort of breast cancer patients. MATERIALS/METHODS: Tumors were resected from patients with either primary or metastatic breast cancer and implanted into immunodeficient mice to establish PDX models. Successfully engrafted PDX models were expanded and randomized for drug sensitivity testing. Tumor growth inhibition and tumor regression were captured and results were correlated with a patient’s clinical response. In some cases, PDX results were used to personalize cancer treatment and some patients used PDX-directed treatments over multiple lines of therapy. RESULTS: A total of 42 tumors from 40 patients were implanted resulting in 21 successfully engrafted PDX models (50% engraftment rate). Notably, engraftment rates were much higher for patients with triple negative breast cancer (TNBC) and resulted in 7 successful PDX models from 8 TNBC patients (87.5% engraftment rate). Drug sensitivity testing was offered to patients with established PDX models. Drugs and drug combinations tested included standard and nonstandard chemotherapy as well as biologics. At that time of this publication, 4 patients (3 TNBC and 1 HER2+) with completed drug sensitivity tests also had clinical data available resulting in 7 clinical correlations; 4 retrospective and 3 prospective. In all 7 cases, the PDX model accurately predicted patient clinical response demonstrating an accuracy of 100%. Five of the drug tests predicted drug sensitivity and 2 tests predicted resistance, indicating the potential of the PDX platform to predict for both sensitivity and resistance to therapy. The 3 prospective correlations resulted in concordant clinical benefit in 2 patients for duration greater than 6 months each. CONCLUSIONS: These data support the use of the personalized PDX model as a platform for therapeutic decision making that can guide treatment for patients with breast cancer. A prospective clinical trial in TNBC is currently underway. Citation Format: Lisa Stow, Amanda Katz, Hanna Irie, Elisa Port, Justin Stebbing, Daniel Ciznadija, Angela Davies, Keren Paz. Patient-derived xenografts accurately predict patient response in breast cancer patients [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 P3-06-31.
Background: Protein kinase C theta, (PRKCQ/PKCθ) is a serine/threonine kinase that is highly expr... more Background: Protein kinase C theta, (PRKCQ/PKCθ) is a serine/threonine kinase that is highly expressed in a subset of triple-negative breast cancers (TNBC) and promotes their growth, anoikis resistance, epithelial-mesenchymal transition (EMT), and invasion. Here, we show that PRKCQ regulates the sensitivity of TNBC cells to apoptosis triggered by standard-of-care chemotherapy by regulating levels of pro-apoptotic Bim. Methods: To determine the effects of PRKCQ expression on chemotherapy-induced apoptosis, shRNA and cDNA vectors were used to modulate the PRKCQ expression in MCF-10A breast epithelial cells or triple-negative breast cancer cells (MDA-MB231Luc, HCC1806). A novel PRKCQ small-molecule inhibitor, 17k, was used to inhibit kinase activity. Viability and apoptosis of cells treated with PRKCQ cDNA/shRNA/inhibitor +/-chemotherapy were measured. Expression levels of Bcl2 family members were assessed. Results: Enhanced expression of PRKCQ is sufficient to suppress apoptosis triggered by paclitaxel or doxorubicin treatment. Downregulation of PRKCQ also enhanced the apoptosis of chemotherapy-treated TNBC cells. Regulation of chemotherapy sensitivity by PRKCQ mechanistically occurs via regulation of levels of Bim, a pro-apoptotic Bcl2 family member; suppression of Bim prevents the enhanced apoptosis observed with combined PRKCQ downregulation and chemotherapy treatment. Regulation of Bim and chemotherapy sensitivity is significantly dependent on PRKCQ kinase activity; overexpression of a catalytically inactive PRKCQ does not suppress Bim or chemotherapy-associated apoptosis. Furthermore, PRKCQ kinase inhibitor treatment suppressed growth, increased anoikis and Bim expression, and enhanced apoptosis of chemotherapy-treated TNBC cells, phenocopying the effects of PRKCQ downregulation. Conclusions: These studies support PRKCQ inhibition as an attractive therapeutic strategy and complement to chemotherapy to inhibit the growth and survival of TNBC cells.
Introduction: Protein tyrosine kinase 6 (PTK6) is a non-receptor tyrosine kinase that is highly e... more Introduction: Protein tyrosine kinase 6 (PTK6) is a non-receptor tyrosine kinase that is highly expressed in Human Epidermal Growth Factor 2 + (Her2 +) breast cancers. Overexpression of PTK6 enhances anchorage-independent survival, proliferation, and migration of breast cancer cells. We hypothesized that PTK6 inhibition is an effective strategy to inhibit growth and survival of Her2 + breast cancer cells, including those that are relatively resistant to Lapatinib, a targeted therapy for Her2 + breast cancer, either intrinsically or acquired after continuous drug exposure. Methods: To determine the effects of PTK6 inhibition on Lapatinib-resistant Her2 + breast cancer cell lines (UACC893R1 and MDA-MB-453), we used short hairpin ribonucleic acid (shRNA) vectors to downregulate PTK6 expression. We determined the effects of PTK6 downregulation on growth and survival in vitro and in vivo, as well as the mechanisms responsible for these effects. Results: Lapatinib treatment of "sensitive" Her2 + cells induces apoptotic cell death and enhances transcript and protein levels of Bim, a pro-apoptotic Bcl2 family member. In contrast, treatment of relatively "resistant" Her2 + cells fails to induce Bim or enhance levels of cleaved, poly-ADP ribose polymerase (PARP). Downregulation of PTK6 expression in these "resistant" cells enhances Bim expression, resulting in apoptotic cell death. PTK6 downregulation impairs growth of these cells in in vitro 3-D Matrigel TM cultures, and also inhibits growth of Her2 + primary tumor xenografts. Bim expression is critical for apoptosis induced by PTK6 downregulation, as co-expression of Bim shRNA rescued these cells from PTK6 shRNA-induced death. The regulation of Bim by PTK6 is not via changes in Erk/MAPK or Akt signaling, two pathways known to regulate Bim expression. Rather, PTK6 downregulation activates p38, and pharmacological inhibition of p38 activity prevents PTK6 shRNA-induced Bim expression and partially rescues cells from apoptosis. Conclusions: PTK6 downregulation induces apoptosis of Lapatinib-resistant Her2 + breast cancer cells by enhancing Bim expression via p38 activation. As Bim expression is a critical biomarker for response to many targeted therapies, PTK6 inhibition may offer a therapeutic approach to treating patients with Her2 targeted therapy-resistant breast cancers.
Background/Rationale: Sensitivity to chemotherapy consistently remains a strong predictor of long... more Background/Rationale: Sensitivity to chemotherapy consistently remains a strong predictor of long term outcomes and survival for patients diagnosed with triple negative breast cancer (TNBC). Patients who do not achieve a complete pathological response to pre-operative, neoadjuvant chemotherapy are at increased risk for metastatic recurrence. Clinical trials with targeted therapies and immunotherapies aim to reduce this risk of recurrence for this patient population. As part of our ongoing prospective study of patients with TNBC that involves serial blood collections and tissue collections (pre-treatment biopsy and post-neoadjuvant surgical specimen) from the time of initial diagnosis, we are particularly focused on those patients with residual disease following neoadjuvant treatment. Comprehensive tissue and cell-free DNA (cfDNA)/circulating tumor cell (CTC) profiling of these patients could lead to insights into mechanisms of chemotherapy resistance and new treatment strategies to prevent recurrences. In addition to genomic profiling, we have analyzed PD-L1 expression on tissue and CTC’s which may contribute to improve targeted utilization of immunotherapies for patients with early stage, high-risk TNBC. Methods: Patients diagnosed with TNBC (stage 1-3) are consented for this prospective study. Serial collections of blood are obtained at time of initial diagnosis, following neoadjuvant chemotherapy or upfront surgery and at 6 month intervals following completion of all active therapy. cfDNA/CTC are isolated using Cynvenio’s Liquid Biopsy platform and sequenced on a rolling basis with Oncomine V3 panel. Tissue from initial biopsy and surgical resection are also collected and sequenced. PD-L1 staining of breast tumor tissue and CTC is performed using antibody SP-142 and atezolizumab, respectively. Clinical outcomes (response to chemotherapy and recurrence data) are also recorded. Results: 30 patients are currently being followed. Of these 24 patients were treated with neoadjuvant chemotherapy and 10/24 (42%) had a pathological complete response (pCR). For the patients treated with neoadjuvant chemotherapy whose pre-treatment samples have been sequenced, 3/6 (50%) of patients who did not achieve a pCR had pre-treatment detectable mutations in cfDNA/CTC in contrast to 3/9 (33%) patients who achieved a pCR. Furthermore, all 6 patients who had residual disease had at least one blood collection with detectable cfDNA/CTC mutations following completion of all active breast cancer therapy. For the five patients with post-neoadjuvant residual disease whose surgical specimens have been stained for PD-L1 expression, 4/5 (80%) are PD-L1 positive (>1%) either in the tumor or infiltrating leukocyte population. PD-L1 positive circulating CTC’s were also detected in 1 of these patients with PD-L1 positive residual disease thus far. Conclusions: Prospective serial analysis of cfDNA/CTC may identify patients who are at higher risk for incomplete response to neoadjuvant therapy or metastatic recurrence. PD-L1 staining of post-neoadjuvant residual cancer and/or CTC’s may help identify high risk patients most likely to benefit from adjuvant immunotherapy. Citation Format: Hanna Yoko Irie, Paul Schmidt, Elisa Port, Natalie Berger, Paula Klein, Yayoi Kinoshita, Alan Soto, Kereeti Pisapati, Ronald Couri, Olivia Kolodka, Hanane Arib, Robert Sebra, Michael J Donovan. Prospective genomic and PD-L1 profiling of patients with residual triple negative breast cancer after neoadjuvant chemotherapy [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 P5-01-09.
e24108Background: Patients with early stage triple negative breast cancer (TNBC) are treated with... more e24108Background: Patients with early stage triple negative breast cancer (TNBC) are treated with multimodality therapy (chemotherapy, surgery, radiation). Cell-free DNA (cfDNA) and circulating tum...
e23070 Background: Serial liquid biopsy assessment provides a unique platform for detecting exist... more e23070 Background: Serial liquid biopsy assessment provides a unique platform for detecting existing and / or emergent resistance mutations; it may be particularly beneficial when patients begin to progress on otherwise effective therapy. We aimed to determine the utility of such an approach for detection of tumor genetic alterations at multiple points during the clinical course of patients diagnosed with breast cancer. Methods: Twenty patients diagnosed with stage I-IV breast cancer (50% with triple negative disease) receiving treatment at the Dubin Center of Mount Sinai were consented for serial CTC/cfDNA collections between October 2015 and November 2016. Circulating tumor cell (CTC)/cell-free DNA (cfDNA) were isolated using Cynvenio’s Liquid Biopsy platform and sequenced utilizing the Hotspot/Oncomine panels. DNA from corresponding patient tumors, when available, was also sequenced. Results: 25% of patients had at least one known pathogenic mutation detected in either cfDNA or CTC DNA in at least one collection; all patients had stage IV disease at collection. Pathogenic mutations detected were in p53 (15%), PIK3CA (10%) and Smad4 (5%). For those patients with available tumor tissue, the same pathogenic mutation was detected in the primary tumor. Mutations were more often detected in cfDNA rather than CTC DNA. Finally, known pathogenic mutations were more consistently detected in serial collections with clinical disease progression and resistance to treatment. Conclusions: Pathogenic mutations were identified in 25% of patients, more frequently in cfDNA and not in every collected sample, supporting serial collection studies to monitor response. Presence of same pathogenic mutations in the patient’s primary tumor suggest a role for surveillance in early stage, as well as advanced disease.
e12594Background: Obesity and weight gain are significant concerns for breast cancer survivors. O... more e12594Background: Obesity and weight gain are significant concerns for breast cancer survivors. Obesity at diagnosis of breast cancer is an established negative prognostic factor and post-diagnosis...
Background: Niraparib is a selective poly(ADP-ribose) polymerase 1/2 inhibitor that has demonstra... more Background: Niraparib is a selective poly(ADP-ribose) polymerase 1/2 inhibitor that has demonstrated antitumor activity in advanced triple-negative breast cancer (TNBC) in combination with a programmed cell death 1 inhibitor, with the greatest clinical activity seen in tumors with breast cancer susceptibility gene (BRCA) mutations. Pharmacologically, niraparib has demonstrated a wide volume of distribution and high cell membrane permeability. In breast and ovarian cancer xenograft mouse models, niraparib achieved tumor exposures that were 3.3 times greater than plasma exposure. The objective of this study is to evaluate the antitumor activity of single-agent niraparib in the neoadjuvant treatment of patients with localized, human epidermal growth factor receptor 2 (HER2)-negative, BRCA-mutated breast cancer. The relative concentration of niraparib in tumor versus plasma was also assessed. Methods: Eligible patients were ≥18 years old, with HER2-negative, BRCA-mutated (germline or so...
108600, a novel CK2/DYRK1/TNIK inhibitor, targets and inhibits cancer stem cells (CSC) in triple ... more 108600, a novel CK2/DYRK1/TNIK inhibitor, targets and inhibits cancer stem cells (CSC) in triple negative breast cancer (TNBC), inhibiting tumor growth and metastases in patient-derived xenograft models. CSC’s have been shown to promote immune evasion of several types of cancer. Specifically, over-expression of CK2 has been shown to promote intratumoral recruitment of myeloid derived suppressor cells. We investigated the effects of 108600 treatment on the immune microenvironment of triple negative breast cancer since targeting CSC’s could promote favorable anti-tumor immune responses and mechanistically contribute to tumor growth inhibition. Methods:C57BL/6 mice bearing murine triple negative E0771 tumors were generated by orthotopic injection and treated either with vehicle control or 108600 for 5 days. Tumor growth was assessed by daily caliper measurement All tumors were recovered at endpoint, and processed for RNA sequencing, flow cytometry or Western blot analysis. Results:1086...
Background/Rational: Patients with triple negative breast cancers (TNBC) have limited therapeutic... more Background/Rational: Patients with triple negative breast cancers (TNBC) have limited therapeutic options beyond conventional chemotherapy. Unfortunately, high-risk for metastatic recurrence and chemotherapy resistant diseases cause the worst 5-year survival rate in patients with TNBC, which have been significant clinical challenges. Novel therapeutic targets or strategies to combat metastasis and chemotherapy resistance are necessary to improve quality of life and outcomes for patients with high risk TNBC. Epithelial-to-mesenchymal transition (EMT) and anoikis resistance are processes recognized as contributing to enhanced metastatic potential and treatment resistance. A subset of TNBC exhibits mesenchymal gene signatures and phenotypes that may be associated with high metastatic recurrence, chemotherapy resistance and immunosuppression. In a functional genomic screen, we identified several candidates as novel regulators of EMT and anoikis sensitivity of TNBC cells. We have focused...
TPS1103Background: Overexpression or amplification of HER2 occurs in approximately 15 – 20% of pa... more TPS1103Background: Overexpression or amplification of HER2 occurs in approximately 15 – 20% of patients and about half of these tumors are hormone receptor (HR) positive. Studies suggest that this 10% of all breast cancer cases may derive less benefit from endocrine therapy than those with HR+ disease without HER2 overexpression. The use of aromatase inhibitors in the metastatic setting is well established while significant improvement in overall survival has been established with the use of trastuzumab or pertuzumab in HER2-overexpressing tumors. To date, no studies have examined the combination of endocrine therapy, palbociclib, and dual HER2 therapy with pertuzumab and trastuzumab in this patient population. Trial Design: Multicenter, Phase I/II Trial of Anastrozole, Palbociclib, Trastuzumab and Pertuzumab in HR-positive, Her2-positive Metastatic Breast Cancer. Eligibility Criteria: Stage IV HR+, HER2+ breast cancer patients. Specific Aims: Phase I: To determine the maximum dose tolerated of palbocicli...
e14307 Background: Mutation-derived tumor antigens (MTAs) arise as a direct result of somatic var... more e14307 Background: Mutation-derived tumor antigens (MTAs) arise as a direct result of somatic variations that occur during carcinogenesis and can be characterized via genetic sequencing and used to identify MTAs. We developed a platform for a fully-personalized MTA-based vaccine in the adjuvant treatment of solid and hematological malignancies. Methods: This is a single-arm, open label, proof-of-concept phase I study designed to test the safety and immunogenicity of Personalized Genomic Vaccine 001 (PGV001) that targets up to 10 predicted personal tumor neoantigens based on patient’s HLA profile (ClinicalTrials.gov: NCT02721043). Results: Patients who completed vaccination with PGV001_002 (head and neck squamous cell cancer) received 10 doses of vaccine comprising 10 long peptides (LP) combined with poly-ICLC (toll-like receptor-3 agonist) intradermally. Vaccine-induced T-cell responses were determined at weeks 0 and 27 (before and after treatment, respectively), ex vivo by interfer...
TPS1109 Background: Triple negative breast cancer (TNBC) is an aggressive disease with unmet clin... more TPS1109 Background: Triple negative breast cancer (TNBC) is an aggressive disease with unmet clinical needs. Women with TNBC tend to be younger and demonstrate early recurrence, higher histological grade, higher rate of visceral metastasis and increased mortality rates when compared to hormone positive breast cancer. Prognosis for metastatic TNBC is especially poor. Due to lack of targeted therapies, there is no standard treatment of choice for triple negative breast cancer and chemotherapy remains the accepted standard. Many chemotherapeutic agents have been reported to have clinical activity either as single agent or in combination. Seventy percent of breast cancers with BRCA-1 germline mutations are triple negative, which suggests a shared carcinogenic pathway between them. In preoperative and metastatic settings, both TNBC and BRCA-1 associated breast cancers are particularly sensitive to DNA cross-linking agents such as platinum compounds due to defective DNA repair by homologo...
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