bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract A22: Role of cap-dependent translation in response to upstream kinase-targeted therapy in colorectal cancer
Authors: Ye Qing , Cai Weijia , Evers B. Mark , Solit David , Rosen Neal , She Qing-Bai
Published: May 2015

Mutational activation of the PI3K/AKT and RAS/RAF/MEK/ERK pathways is associated with colorectal cancer (CRC) progression and metastasis. Several small-molecule inhibitors of PI3K, AKT, RAF and MEK have been tested in the clinic for the treatment of CRC but have shown only limited activity as a single agent. We find that a potential mechanism of AKT or ERK-independence is associated with redundant activation of eIF4E-initiated cap-dependent translation mediated by convergent regulation of the translation repressor 4E-BP1 by the AKT and ERK pathways. Combined inhibition of both pathways exhibits synergistic anti-CRC effects, both in vitro and in vivo, by effectively inhibiting cap-dependent translation via maximal activation of 4E-BP1 function. Specifically, we identify that survivin is a key translationally-regulated target of both pathways through convergence on the mTORC1/4E-BP1/eIF4E axis, and continuous translation of survivin by AKT and ERK signaling is crucial for CRC progression to metastasis. These findings reveal that the cap-dependent translation functions as a critical regulatory node that integrates oncogenic AKT and ERK signals for metastatic progression of CRC. Thus, targeting cap-dependent translation that could simultaneously block upstream oncogenic signals and their downstream targets may provide a promising therapeutic strategy for advanced CRC.

Citation Format: Qing Ye, Weijia Cai, B. Mark Evers, David Solit, Neal Rosen, Qing-Bai She. Role of cap-dependent translation in response to upstream kinase-targeted therapy in colorectal cancer. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr A22.
Abstract A33: Combined therapy of a novel anti-NOTCH2/3 antibody with paclitaxel inhibits tumor growth in a patient-derived breast tumor xenograft
Authors: Wei Jie , Cain Jennifer , Shah Jalpa , Wallace Breanna , Tang Tracy , Wang Min , Murriel Christopher , Belinda Cancilla , Gurney Austin , Sato Aaron , Lewicki John , Kapoun Ann , Hoey Tim
Published: May 2015

Cancer stem cells (CSCs) have been identified as the small subpopulation of cells in many cancers and are thought to be responsible for cancer initiation, progression, metastasis, recurrence and drug resistance. The NOTCH pathway, comprised of ligands JAG1, JAG2, DLL1, DLL3 and DLL4 and receptors NOTCH1, NOTCH2, NOTCH3 and NOTCH4, plays a critical role in stem cell signaling, cell proliferation, survival, apoptosis, and differentiation. Because of the existing body of data that implicates aberrant NOTCH pathway activation in resistance to chemotherapeutic agents in epithelial and hematologic tumors, we hypothesized that NOTCH inhibition would enhance the anti-tumor activity of chemotherapeutic agents.

We have identified a NOTCH3 activating mutation in a patient breast cancer and developed a xenograft tumor model from the primary patient sample, OMP-B37. The combination of paclitaxel and OncoMed's anti-Notch2/3 antibody, OMP-59R5, inhibited the tumor growth of OMP-B37 xenograft tumors. In addition, we found that treatment with OMP-59R5 drove changes in tumor heterogeneity as indicated by the increased expression of markers associated with a mature cellular fate. The down-regulation of tumor growth promoting genes and NOTCH pathway markers was observed with OMP-59R5 treatment. The enhanced activity of combined OMP-59R5 and paclitaxel therapy in patient-derived tumor xenografts suggests that there is therapeutic potential in combining targeted NOTCH pathway inhibition with chemotherapeutic agents.

Citation Format: Jie Wei, Jennifer Cain, Jalpa Shah, Breanna Wallace, Tracy Tang, Min Wang, Christopher Murriel, Cancilla Belinda, Austin Gurney, Aaron Sato, John Lewicki, Ann Kapoun, Tim Hoey. Combined therapy of a novel anti-NOTCH2/3 antibody with paclitaxel inhibits tumor growth in a patient-derived breast tumor xenograft. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr A33.
Abstract A50: Crotamine derived fusion short-peptides and their effect on melanoma and breast cancer cells cultured in vitro
Authors: Mambelli Nicole Caroline , De-Sá-Júnior Paulo Luis , Ferreira Adilson Kleber , Azevedo Ricardo Alexandre , Câmara Diana Aparecida , Kerkis Irina
Published: May 2015

The search for molecules with therapeutic potential against cancer is a crucial issue to reduce the amount of death in human population around the world. Previously, we showed that crotamine, a natural polypeptide from the venom of the rattlesnake Crotalus durissus terrificus, has ability to induce cancer cells apoptosis in vitro, as well as, delay and inhibit melanomas formation in vivo in mice. In order to reduce crotamine length and toxicity, while maintaining its anti-cancer properties, two short peptides were designed and synthetized. Such short peptides represent an intermediate potential step toward to the development of drugs targeted cancer death. The aim of present study was to analyze pro-apoptotic activity of both of these peptides (1 and 2), composed by crotamine (crot.) and BAX (pro-apoptotic protein from BCL2 family) both derived sequences in melanoma and breast cancer cells in vitro. Melanoma and breast cancer cells (MEL-85, A2058, B16-F10 and SKBR3) were used. The MTT assay was performed after addition of both of these peptides used in different concentrations into cancer cells. The expression of proteins (PARP, Cleaved - Caspase 3, Caspase 3, Phospho - BAD) was evaluated by western blotting. Flow cytometry was performed to evaluate the cell cycle. The mitochondria potential was also verified before and after peptides addition. Morphologic changes, such as, detachment from substrate, cell contraction, loss of inter-cell elongations and several others effects were observed in cancer cells after 24 hours of incubation with peptides. At that time, the peptides exhibit cytotoxic activity as verified by MTT assay. Cell cycle analyses demonstrated that they decrease the timing of G2/M phases, while increasing a sub-G0/G1 phase. Unexpectedly, both peptides increase mitochondria potential of cancer cells, when compared with control cultures (without addition of peptides). Increase of expression pro-apoptotic proteins, such as, cleaved Caspase 3 and PARP was evidenced in cancer cells after addition of peptide -1, while Phospho-BAD was increased after addition of peptide - 2. Our data suggest that both peptides are efficient to trigger cell death in melanoma and breast cancer cells in vitro. Crot alone was not able to induce such changes in cancer cells.

Citation Format: Nicole Caroline Mambelli, Paulo Luis De-Sá-Júnior, Jr., Adilson Kleber Ferreira, Ricardo Alexandre Azevedo, Diana Aparecida Câmara, Irina Kerkis, Sr.. Crotamine derived fusion short-peptides and their effect on melanoma and breast cancer cells cultured in vitro. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr A50.
Abstract A53: Integrative data analysis of colorectal cancer reveals the frequently metastatic sample cluster
Authors: Tsuji Shingo , Midorikawa Yutaka , Seki Motoaki , Takayama Tadatoshi , Sugiyama Yasuyuki , Aburatani Hiroyuki
Published: May 2015

High-throughput biological technologies enabled to identify cancer related key molecules and subclasses. However, single experiment could only elucidate one feature of the tumor pathway. In order to identify the clusters and pathways significant for cancer progression, we performed integrated analysis using gene expression and DNA methylation profiles of colorectal cancer samples. Extracting core CpG sites from CpG island with our newly developed method, iClusterPlus, one of integrated analyses methodologies, was applied to expression array and methylation profiling data and 116 colorectal cancer samples were divided into various cluster size (2≤k≤11). We examined clusters (k=3 and k=6), and found that each cluster (k=3) clearly corresponds to three groups consisting of the combination of two clusters in cluster (k=6) with different prognosis. Expression profiles of two clusters in each group were significantly different, which suggests that aberrant DNA methylation is accumulated during the early stage of cancer, while alteration of gene expression profile is the late event of cancer progression. Furthermore, network-based analysis using expression profiles demonstrated that modules including hnRNP family was down-regulated in one of the cluster (k=6) which frequently harbored liver metastasis and poor prognosis. Integrated clustering analysis applied to multidimensional methods is available to identify disease characteristics such as survival rate and distant metastasis, which might be valuable for improving cancer therapy.

Citation Format: Shingo Tsuji, Yutaka Midorikawa, Motoaki Seki, Tadatoshi Takayama, Yasuyuki Sugiyama, Hiroyuki Aburatani. Integrative data analysis of colorectal cancer reveals the frequently metastatic sample cluster. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr A53.
Abstract B03: Cisplatin-resistant cells possess collateral sensitivity to folate antimetabolites
Authors: Chang Shih-Shin , Yamaguchi Hirohito , Hung Mien-Chie
Published: May 2015

Cisplatin is widely used as a first-line chemotherapeutic agent for lung cancers. Although effective initially, lung cancer cells eventually acquire resistance to cisplatin, causing tumor recurrence. Understanding mechanisms that govern cisplatin resistance is expected to improve therapeutic efficacy in lung cancer patients. Although various studies using cisplatin-resistant cell lines have revealed possible mechanisms of resistance, the applicability of these mechanisms in a clinical setting are debatable. One possible reason for this discrepancy may be the use of cell line models which are exposed to unnaturally high doses of cisplatin to yield cells with a resistant phenotype. These cell lines may not be representative of naturally arising cisplatin-resistant cells in tumors that are treated according to a clinically established dose and schedule. Therefore, to improve the experimental model, we have established two new cisplatin-resistant lung cancer cell lines through intermittent low dose challenges that mimic a clinical treatment schedule (one pulse/month for up to six cycles). The resistant cell lines resulting from this procedure demonstrate improved clonogenic potential and sphere-forming properties, suggesting an increase in the population of tumor-initiating cells. Interestingly, via testing with several different anti-cancer drugs, we found that these resistant cells are more sensitive to the antifolate Pemetrexed, in comparison to their parental cells. To conclude, our study suggests that sequential administration of antifolates might be useful in the treatment of lung cancers that have acquired cisplatin resistance.

Citation Format: Shih-Shin Chang, Hirohito Yamaguchi, Mien-Chie Hung. Cisplatin-resistant cells possess collateral sensitivity to folate antimetabolites. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B03.
Abstract B08: New Abelson interactor-1(Abi-1)-driven mechanism of acquired drug resistance
Authors: Chorzalska Anna , Salloum Ibrahem , Marjon Philip , Treaba Diana , Schorl Christoph , John Morgan , Bryke Christine R. , Reagan John , Winer Eric , Olszewski Adam J. , Dubielecka Patrycja M.
Published: May 2015

In hematological malignancies, quiescent leukemic stem cells are responsible for persistence of minimal residual disease and relapse. We have recently identified a new signaling pathway that is significantly dysregulated in imatinib mesylate (IM) resistant leukemic cells (Chorzalska et all, Leukemia in press). A key player in this pathway is Abelson interactor-1 (Abi-1). Abi-1 was originally identified as Abl kinase associating protein that was later confirmed to be one of the Bcr-Abl interactors. Abi-1 was recently shown to interact directly with α4 integrin, which controls lodging of hematopoietic and leukemic stem cells (HSCs/LSCs) in the bone marrow microenvironment. We have recently obtained evidence that Abi-1 plays a role in signaling cross-talk between Bcr-Abl and α4 integrin. We have found that loss of Abi-1 leads to increased adhesion and quiescence, resulting in increased chemoresistance of leukemic CD34+ progenitor cells. Comparison of Abi-1 (ABI-1) and α4 integrin (ITGA4) gene expression in relapsing Bcr-Abl positive CD34+ progenitor cells demonstrated a reduction in Abi-1 and an increase in α4 integrin mRNA in the absence of Bcr-Abl mutations. This inverse correlation between Abi-1 and α4 integrin expression, as well as linkage to elevated phospho-Akt and phospho-Erk signaling, was confirmed in imatinib mesylate (IM) resistant leukemic cells. These results indicate that the α4-Abi-1 signaling pathway may mediate acquisition of the drug resistant phenotype of leukemic cells. Based on our findings, we hypothesize that chemoresistance arises as a consequence of dysregulation of a pathway involving α4 integrin and Abi-1, and is mediated through a previously unknown mechanism that is independent of oncogene activity.

Citation Format: Anna Chorzalska, Ibrahem Salloum, Philip Marjon, Diana Treaba, Christoph Schorl, Morgan John, Christine R. Bryke, John Reagan, Eric Winer, Adam J. Olszewski, Patrycja M. Dubielecka. New Abelson interactor-1(Abi-1)-driven mechanism of acquired drug resistance. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B08.
Abstract B16: Combination of docetaxel with histone deacetylase inhibitor inhibits AR signaling synergistically in hormone-independent 22Rv1 prostate cancer cells
Authors: Kim Ha-Gyeong , Hwang Jung Jin , Kim Choung-Soo
Published: May 2015

Globally prostate cancer is the sixth leading cause of cancer-related death in men, and it is now the first in the United Kingdom and second in the United States. At the early stage, prostate cancer growth and progression depend on androgen receptor (AR) signaling. Therefore, androgen-deprivation therapy (ADT) is effective to patient with prostate cancer by inhibition of androgen synthesis. With time, however, most patients with prostate cancer eventually lose sensitivity to androgen withdrawal and progress to the development of castration-resistant prostate cancer (CRPC). Though docetaxel is a standard of care therapy in CRPC, most of patients develop resistance to this therapy. Therefore, the novel therapeutic strategies and combination therapy are needed to overcome this resistance. In this study, we examined whether histone deacetylase inhibitor (HDACI), suberoylanilide hydroxamic acid (SAHA) might enhance the effect of docetaxel in CRPC. Hormone-independent 22Rv1 cells harboring AR were treated with docetaxel and/or SAHA. Co-treatment of docetaxel and SAHA inhibited the growth of 22Rv1 cells synergistically. Combination treatment decreased the levels of AR, prostate specific antigen (PSA), and anti-apoptotic Bcl-2 proteins (Mcl-1, Bcl-xl) more efficiently compared with docetaxel or SAHA alone, when it analyzed by Western blot. And combination treatment increased activation of caspase-3 remarkably, while docetaxel or SAHA alone increased it slightly. Moreover, immunocytochemistry and analysis of nuclear fractionated proteins showed that combination treatment induced acetylation and bundling of tubulin, inhibiting nuclear accumulation of AR significantly. These results suggested that docetaxel in combination with SAHA inhibited cell growth efficiently and induced apoptosis by repressing expression and translocation to nucleus of AR in 22Rv1 cells, and this combination can be a useful therapeutics for the treatment of CRPC patients.

Citation Format: Ha-Gyeong Kim, Jung Jin Hwang, Choung-Soo Kim. Combination of docetaxel with histone deacetylase inhibitor inhibits AR signaling synergistically in hormone-independent 22Rv1 prostate cancer cells. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B16.
Abstract B24: Attenuated expression of a novel mitochondrial and metabolic gene contributes to acquired gefitinib resistance in lung tumors
Authors: Okon Imoh S. , Coughlan Kathleen A. , Zou Ming-Hui
Published: May 2015

Therapeutic benefits provided by tyrosine kinase inhibitors (TKIs), such as Gefitinib (Iressa) and Erlotinib (Tarceva) have been limited by resistance which contributes to treatment failure and cancer-related mortality. Dysregulated metabolism (Warburg effect), a property of cancer cells has been linked to drug resistance, but the mechanisms remain unknown. In this study, MRC-9 (normal “non-cancer” cells), as well as A549, H1650, H1792 and H1975 lung adenocarcinoma cell lines (from ATCC; Manassas, VA) were used in order to examine those process(es) involved in the development of gefitinib resistance. Gefitinib is a specific, targeted agent against the epidermal growth factor receptor (EGFR) that competes for ATP-binding sites in the tyrosine activation domain of the receptor. Gefitinib-resistant H1650G cells were generated by subjecting parental H1650 cells to chronic gefitinib exposure for 12-16 weeks, and continuous culture under gefitinib selection. Consistent with existing literature, micro-array analysis of gefitinib-resistant H1650G cells confirmed differential expression of epithelial-mesenchymal transition (EMT) genes, such as vimentin, fascin1 and keratin19 compared to parental H1650 cells. Importantly, we uncovered the loss of a mitochondrial/metabolic gene intimately involved with glycolysis as a contributor to acquired gefitinib resistance in lung cancer cell lines and clinical specimens. Loss of expression of the novel target correlated with decreased ATP generation, and concomitant up-regulation of autophagy marker (LC3II), consistent with a compensatory mechanism of energy generation. Depletion (siRNA) of EGFR in parental H1650 cells was employed to mimic attenuated expression of the receptor due to sustained gefitinib treatment in H1650G cells, and correlated with decreased expression of the mitochondrial/metabolic target. This observation connects the EGFR signaling pathway with a novel mitochondrial/metabolic gene, and provides new insight into the development of acquired gefitinib resistance and adaptations by resistant cancer cells. The findings identify a novel potential target for therapeutic intervention, or biomarker functions that would enable informed patient selection with respect to gefitinib resistance.

Citation Format: Imoh S. Okon, Kathleen A. Coughlan, Ming-Hui Zou. Attenuated expression of a novel mitochondrial and metabolic gene contributes to acquired gefitinib resistance in lung tumors. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B24.
Abstract B33: Integration of genome-wide datasets identifies SOX10 as a lineage-specific genetic dependency in melanoma
Authors: Wong Terence C. , Johannessen Cory M. , Garraway Levi A.
Published: May 2015

Melanoma accounts for less than 5% of skin cancers, but a majority of skin cancer deaths. Genomic studies have firmly established the role of recurrent somatic alterations in the pathogenesis of melanoma, including mutations in BRAF, NRAS, TP53, PTEN, and CDKN2A. While the discovery of activating mutations in BRAF in over 60% of melanomas has led to the development of FDA-approved BRAF and MEK inhibitors that induce dramatic responses in BRAF V600-mutant melanomas, the inevitable resistance to BRAF/MEK inhibitors necessitates a greater understanding of melanoma biology and genetics. By integrating genome-wide functional genomic and expression data, we have identified SOX10 as a lineage-specific genetic dependency in melanoma. SOX10 dependency is highly correlated with SOX10 gene expression in melanoma. Subsequent functional in vitro experiments have confirmed the role of SOX10 in the cellular proliferation and growth of melanoma cell lines. The combination of SOX10 depletion with current FDA-approved targeted therapies for melanoma hold promise for the delay or prevention of resistance to these therapeutics and may lead to more durable control of melanoma in human patients.

Citation Format: Terence C. Wong, Cory M. Johannessen, Levi A. Garraway. Integration of genome-wide datasets identifies SOX10 as a lineage-specific genetic dependency in melanoma. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B33.
Abstract B46: Epigenetic alterations associated with platinum resistance in an ovarian cancer cell model
Authors: Samudio-Ruiz Sabrina L. , Granados Michaela L. , Hudson Laurie G.
Published: May 2015

Platinum resistance in ovarian cancer continues to be an impediment to clinical effectiveness. While multiple alterations associated with platinum resistance have been proposed, mechanisms responsible for those alterations, particularly epigenetic alterations, are still under investigation. Epigenetic alterations, specifically epigenetic silencing induced by DNA methylation, to genes involved in drug response is a common occurrence in platinum resistance. We have previously published that activation of the Epidermal Growth Factor Receptor (EGFR) in ovarian cancer cells increases activity of DNA methyltransferases (DNMTs) and extended EGFR activation can also increase global DNA methylation. In a concurrent abstract, we show that acute cisplatin treatment activates the EGFR and increases DNMT activity. Our overarching hypothesis for this work is that the EGFR is a key player in the development of platinum resistance by its ability to regulate DNMT activity and DNA methylation and thereby could be a therapeutic target for preventing acquisition of platinum resistance during chemotherapeutic treatment. Here, we show data obtained using a cellular model of platinum resistance that we have generated in the lab. We show that OVCA 433 cells treated repeatedly with increasing doses of cisplatin acquire resistance and demonstrate resistance in a 3D model which is more indicative of the ovarian cancer cell microenvironment. These cisplatin resistant cells (CPR) also display significantly increased DNMT activity compared to passage control (non-resistant) cells, with modest increases in global DNA methylation. While hyperactivation of the EGFR is not observed in this chronic model of cisplatin treatment, we do see a significant decrease in Copper transporter 1 (CTR1) levels in CPR cells. CTR1 is particularly important in cisplatin drug uptake, thus we believe that platinum resistance in CPR cells is due to downregulation of CTR1 potentially by DNA methylation. Current studies are evaluating DNA methylation of CTR1 and other genes that may be contributing to the development of platinum resistance. Future studies inhibiting the EGFR during cisplatin treatment will be imperative in linking cisplatin induced EGFR activation to the changes in DNMT activity and methylation that we are observing in our model of platinum resistance. This work implicates EGFR driven alterations to DNMT activity and DNA methylation as a novel mechanism for development of platinum resistance.

Citation Format: Sabrina L. Samudio-Ruiz, Michaela L. Granados, Laurie G. Hudson. Epigenetic alterations associated with platinum resistance in an ovarian cancer cell model. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B46.
Abstract B49: Investigating kinase inhibitor resistance mechanisms through quantitative network mapping of the human kinase interactome
Authors: Cheng Feixiong , Zhao Zhongming
Published: May 2015

The human kinases have become one of the most important classes of drug targets in the pharmaceutical industry. More than 20 drugs targeting one or more kinases have been approved for clinical use in a variety of cancers, including lung, breast, melanoma, colorectal, pancreatic, and prostate cancers. However, patients treated with those kinase inhibitors eventually develop resistance, and their prolong survivals are typically only a few months. So far, no general model has emerged to address the kinase inhibitor resistance. In this study, we constructed a systems biology-based framework to catalogue the human kinome (kinases and their interactions), including 538 kinase genes, in the broader context of the human interactome. Specifically, we constructed three networks: a kinase-substrate interaction network containing 7,346 pairs connecting 379 kinases to 36,576 phosphorylation sites in 1,961 substrates, a protein-protein interaction network (PPIN) containing 92,699 pairs, and an atomic resolution PPIN containing 4,278 pairs. We identified the conserved regulatory phosphorylation motifs (e.g., Ser/Thr-Pro) using a sequence logo analysis. We found the typical anticancer target selection strategy that uses network hubs as drug targets might lead to a high adverse drug reaction risk. Furthermore, we found the distinct network centrality of kinases creates a high anticancer drug resistance risk by feedback or crosstalk mechanisms within cellular networks. This notion is supported by the systematic network and pathway analyses that anticancer drug resistance genes are significantly enriched as hubs and heavily participate in multiple signaling pathways. Collectively, this comprehensive human kinome map sheds light on anticancer drug resistance mechanisms and provides an innovative resource for rational kinase inhibitor design.

Note: This abstract was not presented at the conference.

Citation Format: Feixiong Cheng, Zhongming Zhao. Investigating kinase inhibitor resistance mechanisms through quantitative network mapping of the human kinase interactome. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B49.
Abstract B51: Image-based classification of cancer drug combination response surfaces
Authors: Liu Manway , Horn Thomas , Greene Matthew , Lehar Joseph
Published: May 2015

Recent advances in targeted chemotherapy have dramatically improved the survival odds of patients suffering from specific molecular subtypes of cancer. Nonetheless, while a fortunate few enjoy a durable and lasting response to treatment, the majority will eventually relapse after some grace period in remission due to the emergence of drug-resistant cancer cells.

Acquired resistance is a complex phenomenon that likely involves intra-tumoral heterogeneity, tumor-stromal interactions, and natural selection due to the pressure of chemotherapy. One promising approach to overcome resistance involves utilization of two or more drug compounds in combination, where each compound targets a different member of a signaling pathway important in the disease. By targeting more proteins, the hope is that the probability of any particular cancer cell failing to respond will decrease as the barrier to survival increases.

While drug combinations are an exciting and promising direction for chemotherapeutic research, such studies present additional challenges and opportunities. Interpretation of synergistic and efficacious drug combinations is not always straightforward and pairs of drugs may interact in surprising ways that deviate from expectation based on the molecular pathway relationships between their targets. Moreover, the question of which drugs to prioritize for testing in combination is an important one to which there is currently no standard solution. The brute force approach is not cost-effective due to the factorial growth in the number of possible higher-order drug combinations.

In this work, we present and describe an algorithmic approach to (1) predict synergistic and efficacious drug combinations based on pathway relationships between their targets and (2) classify drug combination response surfaces into canonical archetypes of greatest pharmaceutical interest. Our approach borrows from classical work in image analysis and recognition. We trained and tested our algorithm on two publicly available datasets of drug combinations. We further trained on a private dataset of cancer drug combination data and made predictions that were later experimentally validated in vitro. To our knowledge, our approach is the first proof-of-concept algorithm that utilizes the actual shapes of response surfaces to categorize and prioritize drug combinations for further testing.

Citation Format: Manway Liu, Thomas Horn, Matthew Greene, Joseph Lehar. Image-based classification of cancer drug combination response surfaces. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B51.
Abstract B52: A novel personalized therapeutic management in multiple myeloma
Authors: Krishnan Rajeev S. , Luk Frederick , Brown R. D. , Kwan Y. L. , Bebawy Mary
Published: May 2015

Introduction: Multiple Myeloma (MM) is an incurable hematological malignancy affecting plasma cells marked by highly heterogeneous survival rate. Relapse is a significant impediment to the successful treatment of MM clinically. One of the main causes for relapse is drug resistance to cancer chemotherapy. Currently risk stratification to MM sub -groups and categorization of complete response to therapy are assessed based on molecular, cytogenetic markers using bone marrow biopsy as available systemic markers are incompetent in this regard. We are exploring the clinical significance of our recent in vitro and in vivo findings of a novel non-genetic basis to MDR whereby tiny vesicles called microparticles (MPs) shed from cancer cell's surface transfer MDR phenotype intercellularly. MP isolated from the blood of patients who suffer from Multiple Myeloma will be phenotyped for resistance, adhesion and dissemination markers and assessed whether these characteristics are predictive of treatment outcome.

Materials and Methods: We have analysed 44 de-identified Multiple Myeloma patients. The platelet free plasma was ultracentrifuged, MM- derived microparticles were identified and quantified with flow cytometry using Annexin V450, CD138 APC, P-glycoprotein -FITC in BD TruCount tubes. Also platelet derived MPs were identified and excluded using CD41a PE and compared to age-matched healthy volunteers. Western blot analysis was conducted on microparticle lysate probing for the presence of Lung-resistance related protein (LRP).

Results: Plasma cell derived MPs were identified based on the CD138 expression from the peripheral blood plasma of MM patients. The number of systemic microparticles was found to be significantly higher in MM patients compared to the healthy volunteers. Also the systemic microparticles carried the drug resistance markers.

Conclusions: There are elevated numbers of microparticles in MM that potentially correlate with tumour aggressiveness and they carried MDR phenotypes systemically. Phenotyping MM –derived microparticles holds the potential for a non-invasive personalised systemic biomarker to predict therapeutic response.

Citation Format: Rajeev S. Krishnan, Frederick Luk, R. D. Brown, Y. L. Kwan, Mary Bebawy. A novel personalized therapeutic management in multiple myeloma. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B52.
Abstract IA04: Using comprehensive proteomic approaches to map signaling adaptations to BRAF and BRAF/MEK inhibition
Authors: Fedorenko Inna V. , Paraiso Kim H.T. , Fang Bin , Koomen John M. , Smalley Keiran S.M.
Published: May 2015

Although small molecule inhibitors of BRAF have shown great promise in advanced melanoma, resistance is commonplace. Many patients with acquired BRAF and BRAF/MEK inhibitor resistance develop disease at new sites, suggesting that drug-induced selection pressure drives metastasis. Here we used mass spectrometry-based phosphoproteomic screening and network modeling to uncover two novel adaptations to BRAF inhibitor therapy. The first involved ligand-independent EphA2 signaling that led to the adoption of an invasive/metastatic phenotype. The EphA2-mediated invasion was epigenetically mediated, AKT-dependent and was readily reversible upon removal of drug as well as through PI3K or HDAC inhibition. In a human melanoma mouse xenograft model, chronic BRAF inhibition led to the development of metastases, which stained positively for EphA2. A second phosphoproteomic screen showed BRAF inhibition to enhance the survival of both melanoma cells and fibroblasts through the induction of fibronectin (FN)/integrin α5β1 signaling. Adhesion to FN amplified the adaptive EGFR, HER2 and c-MET signals required for PI3K/AKT-mediated survival when BRAF was inhibited. At the same time, BRAF inhibition led, directly and indirectly, to the paracrine release of HGF and neuregulin from fibroblasts, with TGF-β release from the melanoma cells increasing both fibroblast differentiation and survival. These effects were partly mediated through paradoxical MAPK activation in the fibroblasts and could be reversed through BRAF/MEK inhibition. Thus, we have used comprehensive phosphoproteomics to identify two key non-genetic adaptations to BRAF inhibitor therapy that offer new insights into the process of therapeutic escape.

Citation Format: Inna V. Fedorenko, Kim H.T. Paraiso, Bin Fang, John M. Koomen, Keiran S.M. Smalley. Using comprehensive proteomic approaches to map signaling adaptations to BRAF and BRAF/MEK inhibition. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr IA04.
Abstract IA11: Using genomics to study preexisting resistance
Authors: Mardis Elaine R.
Published: May 2015

High depth sequencing with next-generation technology permits the examination of tumor-derived DNA for evidence of pre-existing, therapy resistance-conferring alterations. Several technical challenges must be addressed to overcome the inherent limitations of assays from pre-treatment biopsies. Specific computational tools are required for accurate assessment of therapy-related alterations and changes in tumor heterogeneity. Approaches that address the assay-related difficulties and the computational analyses required for these analyses will be illustrated by several examples from our studies.

Citation Format: Elaine R. Mardis. Using genomics to study preexisting resistance. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr IA11.
Abstract PR01: Adaptive resistance of patient-derived ovarian cancer cells to PI3K/mTOR inhibition
Authors: Zervantonakis Ioannis , Chen Hsing-Yu , Muranen Taru , Liu Joyce , Drapkin Ronny , Matulonis Ursula , Brugge Joan
Published: May 2015

Relapse due to drug resistance remains a major challenge for successful cancer treatment despite advances in chemotherapy efficacy and the development of targeted therapies. We have previously reported a therapy-induced adaptive response that is associated with treatment resistance and are investigating whether this adaptive response program could be targeted to increase treatment efficacy (Muranen et al, Cancer Cell 2012). The PI3K pathway is amplified in high-grade serous ovarian tumor and represents an attractive target in this cancer subtype. We found that both in vitro and in vivo exposure of patient-derived ovarian cancer cells to the PI3K/mTOR dual inhibitor GNE-493 increases the levels of the anti-apoptotic Bcl-2 protein, and multiple tyrosine kinase receptors, such as EGFR and HER2. Concurrent treatment of these cancer cells with GNE-493 and ABT737 (a Bcl-2 and Bcl-xl dual inhibitor) causes a reduction in cell number and increased cell death. Ongoing studies are underway to comprehensively characterize the adaptive response signature of a panel of patient-derived ovarian cancer cells and study whether targeting multiple different upregulated proteins (e.g. EGFR) may increase PI3K/mTOR treatment efficacy.

Therapy resistance has also been associated with exposure of tumor cells to pro-survival factors secreted by supporting cells in the tumor microenvironment (Straussman et al, Nature 2012 and Wilson et al, Nature 2012). We found that the growth-factors EGF, inflammatory cytokine IL-6 and ascites fluid from ovarian cancer patients induces up-regulation of Bcl-2 as well as IGFR, which masked the adaptive response to PI3K/mTOR inhibitors. We are performing ongoing studies using orthotopic patient-derived ovarian cancer xenografts to investigate the patterns of residual disease in vivo with the ultimate goal to identify whether Bcl-2 targeted drugs will enhance the efficacy of PI3K/mTOR inhibition and whether there is differential sensitivity at distinct anatomical sites (pancreas, diaphragm, peritoneal wall).

Our studies provide a framework to identify adaptive response programs and tumor microenvironment factors in patient-derived ovarian cancer cells that limit treatment efficacy of PI3K/mTOR pathway inhibition and to develop therapies to abrogate this resistance.

Citation Format: Ioannis Zervantonakis, Hsing-Yu Chen, Taru Muranen, Joyce Liu, Ronny Drapkin, Ursula Matulonis, Joan Brugge. Adaptive resistance of patient-derived ovarian cancer cells to PI3K/mTOR inhibition. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr PR01.
Understanding the MIG6–EGFR Signaling Axis in Lung Tumorigenesis
Authors: Izumchenko Evgeny , Sidransky David
Published: May 2015

Summary: With multiple clinical trials under way targeting mutant EGFR in patients with lung cancer, Maity and colleagues address important aspects of a MIG6–EGFR signaling axis using genetically engineered mouse models expressing mutated EGFRs on the MIG6-deficient background. This study extends our understanding of EGFR regulation by MIG6 and reveals that MIG6 antagonizes tumor formation in mutant EGFR–driven lung adenocarcinoma. Cancer Discov; 5(5); 472–4. ©2015 AACR.

See related article by Maity et al., p. 534
The Regulatory Role of Invariant NKT Cells in Tumor Immunity
Authors: McEwen-Smith Rosanna M. , Salio Mariolina , Cerundolo Vincenzo
Published: May 2015

Invariant natural killer T (iNKT) cells are a unique population of T lymphocytes, which lie at the interface between the innate and adaptive immune systems, and are important mediators of immune responses and tumor surveillance. iNKT cells recognize lipid antigens in a CD1d-dependent manner; their subsequent activation results in a rapid and specific downstream response, which enhances both innate and adaptive immunity. The capacity of iNKT cells to modify the immune microenvironment influences the ability of the host to control tumor growth, making them an important population to be harnessed in the clinic for the development of anticancer therapeutics. Indeed, the identification of strong iNKT-cell agonists, such as α-galactosylceramide (α-GalCer) and its analogues, has led to the development of synthetic lipids that have shown potential in vaccination and treatment against cancers. In this Masters of Immunology article, we discuss these latest findings and summarize the major discoveries in iNKT-cell biology, which have enabled the design of potent strategies for immune-mediated tumor destruction. Cancer Immunol Res; 3(5); 425–35. ©2015 AACR.
Highly multiplexed SOMAmer assays as a flexible platform for protein biomarker discovery research
Authors: Saccomano Nicholas A. , Wilcox Sheri , Zichi Dom , Kraemer Stephan , Janjic Nebojsa , Gold Larry , Ayers Deb , Bock Chris , Keeney Tracy , Brody Ed , Vaught Jon
Published: May 2015

SomaLogic presents a transformative proteomic biomarker discovery technology that measures ~1000 human proteins in low volumes (~15 of uL biological sample) with a high-performance, high-throughput, and economical assay. Limits of detection average 1 pM and the overall dynamic range spans 7 logs with ~5% average coefficient of variation. This technology is enabled by a new class of DNA aptamers — “SOMAmers” — that contain novel chemicallymodified nucleotides, which greatly expand the physicochemical diversity of the large combinatorial SELEX libraries from which they are selected. Proteins are measured with a process that transforms a signature of protein concentrations into a representative DNA concentration signature, which is quantified with a DNA microarray. We demonstrate the utility of this technology in a large clinical biomarker discovery study of non-small cell lung cancer, as well as in alternate biological matrices.
A gene expression signature associated with structural differentiation of prostate acini predicts postoperative recurrence of prostate cancer
Authors: Su Jimmy J.-M. , Li Chi-Rong , Lee Michael T.-L. , Chu Patrick Y. W. , Weaver Valerie M. , Tsai Kelvin K.-C.
Published: May 2015

Glandular malignancies such as prostate carcinoma display a considerable heterogeneity in the degree of structural organization while the prognostic role of the associated molecular changes awaits further exploration. Using a three-dimensional (3-D) tissue organization culture model that permits the structural differentiation of prostate glandular epithelium we profiled the transcriptomes of multicellular organoids formed by untransformed prostate epithelial cells (PECs) or prostate carcinoma cells as well as those cultured as cell monolayers. Interrogation into the multiple (n = 6) sets of differentially expressed genes (DEGs) identified that those altered significantly during the structural differentiation process of polarized PEC acini strongly associated with the probability of recurrence in a cohort of 50 prostate cancer patients receiving radical prostatectomy (RP). By contract, the DEGs related to prostate tumor spheroids did not correlate significantly with prognosis. To further explore this association, we prioritized the genes and applied supervised classification algorithms whereby identified a 39-gene structure-associated prognosis signature (SAPS) that shows a remarkable predictivity for the likelihood of post-RP recurrence (overall accuracy 100%, P < 0.001). The SAPS outperformed standard clinicopathological variables, including Gleason scores, as well as existing multigene prognostic predictors of prostate cancer. Our results suggest a distinct contribution by the glandular structural differentiation program to prostate cancer pathology and the usefulness of a robust and biologically relevant genomic predictor of the prognosis of prostate cancer (Supported by NHRI CA-099-PP-19 and Department of Health of Taiwan H99-TD-C-111-004 to KKC).
Insulin-like growth factor receptor 1(IGFIR) is overexpressed in a subset of triple negative breast cancers
Authors: Kline Jessica , Chervoneva Inna , Freydin Boris , solomides Charalambos , Witkiewicz Agnieszka K. , Martin Carl , Peiper Stephen
Published: May 2015

Insulin-like growth factor receptor 1 (IGF-1R) has a key regulatory role in malignancy and is the target of several drugs currently tested in clinical trials. Few studies have shown that IGF-IR expression is associated with estrogen receptor positive breast cancer. However, there are no systematic studies of IGF1R expression in triple negative breast carcinoma (TNBC). The aim of this study was to evaluate IGF1R protein expression and gene amplification in TNBC.

Material and Methods: Ninety-seven TNBC (73 from Caucasian and 24 from African American women) were stained with anti-IGF1R antibody (clone G11, Ventana Medical Systems, Tucson, AZ, USA). IGF1R protein expression was scored according to standardized criteria originally developed for HER 2. Chromogenic in situ hybridization for IGF1R gene was performed on 35 cases using experimental Ventana probe. The tumor was interpreted as positive for gene amplification when the ration of IGF1R gene signal to chromosome 15 signal was ≥ 2.2. For statistical analysis, the IGF1R scores (0, 1, 2, 3) were dichotomized as low (0-2) vs. high (3). Association between IGF1R protein expression and clinicopathologic variables (lymph node metastases, grade, race, age) was analyzed using Fisher's exact test. The association between tumor size and IGF1R expression was analyzed using the Wilcoxon two-sample test. The overall survival was analyzed using LogRank test and Cox proportional hazard model.

Results: A significant association was observed between IGF1R protein expression and IGF1R gene amplification (p<0.001). Respectively, the agreement between IGF1R 3+ protein expression and gene amplification was high (kappa=0.84, 95% CI: 0.62, 1.0; p<0.001). Low (0-2+) IGF1R expression was associated with lymph node metastases (p=0.033) while cases with high (3+) expression had borderline significantly (p=0.080) smaller tumor size. There was no statistically significant association between IGF1R expression and grade or race. In younger patients (<55 years), high IGF1R score was associated with longer survival (HR=0.13; 95% CI: 0.02- 1.00; p=0.050), while in older patients, no significant survival differences were observed between patients with low and high IGF1R scores.

Conclusion: This study suggests that IGF1R is overexpressed and amplified in a subset of TNBC and may be a potential therapeutic target.