bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB-064: Cheminformatics studies to analyze the therapeutic potential of alkaloids from Rhazya stricta
Authors: Sabir Jamal S. , Obaid Abdullah Obaid Y. , Voleti Sreedhara , Bora Roop S. , Hajrah Nahid H. , Omar Abdulkader M. , Saini Kulvinder S.
Published: July 2017

Rhazya stricta is a unique medicinal plant source for many indole alkaloids, non- alkaloids, flavonoids, triterpenes and other unknown molecules with tremendous potential for therapeutic applications against many diseases. In the present article, we generated computational data on predictive properties and activity across two key therapeutic areas of cancer and obesity, and corresponding cheminformatics studies were carried out to examine drugable properties of these alkaloids. Computed physiochemical properties of the 78 indole alkaloids from Rhazya stricta plant using industry-standard scientific molecular modeling software and their predictive anti-cancer activities from reliable web-source technologies indicate their plausible therapeutic applications. Their predictive ADME properties are further indicative of their drug-like-ness. We believe that the top-ranked molecules with anti-cancer activity are clearly amenable to chemical modifications for creating potent, safe and efficacious compounds with the feasibility of generating new chemical entities (NCEs) after pre-clinical and clinical studies.

Keywords: Rhazya stricta, Alkaloids, Physiochemical properties, Druggability, Anticancer molecules, Anti-obesity molecules.

Citation Format: Jamal S. Sabir, Abdullah Obaid Y. Obaid, Sreedhara Voleti, Roop S. Bora, Nahid H. Hajrah, Abdulkader M. Omar, Kulvinder S. Saini. Cheminformatics studies to analyze the therapeutic potential of alkaloids from Rhazya stricta [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-064. doi:10.1158/1538-7445.AM2017-LB-064
Abstract LB-070: Nano self-assemblies of paclitaxel for breast cancer treatment
Authors: Nagesh Prashanth Kumar Bhusetty , Chowdhury Pallabita , Chauhan Sumeeth S. , Hatami Elham , Khan Sheema , Hafeez Bilal , Chauhan Subhash C. , Jaggi Meena , Yallapu Murali M.
Published: July 2017

Objectives: Breast cancer (BC) is second leading cause of cancer-related deaths in the United States. Paclitaxel (Ptx) is an FDA-approved and frequently used chemotherapeutic agent against various cancers, including BC. However its adverse side effects and chemoresistance against it, limits its use in the clinic. Minimizing the toxicity issues of Ptx through nanoparticle technology (such as Ptx bound to human serum albumin nanoformulation, i.e., Abraxane®) is feasible and has displayed encouraging outcomes. With this background, we aim to generate Ptx self-assemblies (PSAs) using various biocompatible polymers and surfactants, and to evaluate its efficacy against BC cells.

Methods: PSAs composed of Ptx dispersion or a core formation with a polymer at a weight ratio of 1:50. The extent of Ptx assembly/binding efficiency was determined using a fluorescence quenching study. FT-IR spectral study was employed to confirm the presence of Ptx in PSAs. The optimal polymers for forming PSAs were identified through measurement of particle size, zeta potential and TEM. Another check point of generating a better PSAs was evaluated by its extent of cellular internalization in BC cells and through hemolytic assay. Finally, the finalized PSAs were examined for in vitro activity in BC cells using proliferation, colony formation, and immunoblotting assays.

Results: We screened 22 biocompatible polymers for PSA formation, out of which 8 were finalized due to excellent Ptx binding profiles, appropriate particle size ranges (40-300 nm), zeta potentials (-14.0 to -4.0 mV), and superior internalization in BC cells. The optimized PSAs exhibited enhanced anti-cancer capability in MCF-7 and MDA-MB-231 BC cells in proliferation and colony formation assays, compared to free Ptx. This was further affirmed through tubulin stabilization studies. Further, PSA treatment in BC cells demonstrates a distinct induction of the expression of apoptosis-associated proteins and distinct downregulation of anti-apoptotic proteins.

Conclusion: Overall this study suggests a simple and feasible Ptxl self-assembly approach for achieving superior anti-cancer activity with Ptx.

Citation Format: Prashanth Kumar Bhusetty Nagesh, Pallabita Chowdhury, Sumeeth S. Chauhan, Elham Hatami, Sheema Khan, Bilal Hafeez, Subhash C. Chauhan, Meena Jaggi, Murali M. Yallapu. Nano self-assemblies of paclitaxel for breast cancer treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-070. doi:10.1158/1538-7445.AM2017-LB-070
Abstract LB-073: Proteomic characterization reveals a molecular portrait of nasopharyngeal carcinoma differentiation
Authors: Xiao Zhefeng , Zhang Guiying , Chen Yongheng
Published: July 2017

Nasopharyngeal carcinoma (NPC) is categorized into three different differentiated subtypes by World Health Organization (WHO). Based on an earlier comparative proteomic database of the three histological subtypes, the study was to deepen our understanding of molecular mechanisms associated with NPC differentiation through bio-information mining. Among the three subtypes were 194 differentially expressed proteins (DEPs) of 725 identified proteins. Two DEPs, heat shock protein family B (small) member 1 (HSPB1) and keratin 5 (KRT5), were validated in a series of NPC tissue samples by using immunohistochemistry. Quantified protein families including keratins, S100 proteins (S100s) and heat shock proteins exhibited characteristic expression alterations. Comparisons of predicted bio-function activation states among different subtypes, including formation of cellular protrusion, metastasis, cell death, and viral infections, were conducted. Canonical pathway analysis inferred that Rho GTPases related signaling pathways regulated the motility and invasion of dedifferentiated NPC. In conclusion, the study explored the proteomic characteristics of NPC differentiation, which could deepen our knowledge of NPC tumorigenesis and allow the development of novel targets of therapeutic and prognostic value in NPC.

Citation Format: Zhefeng Xiao, Guiying Zhang, Yongheng Chen. Proteomic characterization reveals a molecular portrait of nasopharyngeal carcinoma differentiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-073. doi:10.1158/1538-7445.AM2017-LB-073
Abstract LB-080: The histone methyltransferase DOT1L promotes neuroblastoma by regulating gene transcription
Authors: Wong Matthew , Tee Andrew , Milazzo Giorgio , Bell Jessica , Hüttelmaier Stefan , Polly Patsie , Perini Giovanni , Scarlett Christopher J. , Liu Tao
Published: July 2017

Myc oncoproteins exert tumorigenic effects by regulating the expression of target oncogenes. Histone H3 lysine 79 (H3K79) methylation at Myc-responsive elements of target gene promoters is a strict prerequisite for Myc-induced transcriptional activation. DOT1L is the only known histone methyltransferase that catalyses H3K79 methylation. Here, we showed that N-Myc up-regulated DOT1L mRNA and protein expression by binding to the DOT1L gene promoter. Knocking down DOT1L reduced mRNA and protein expression of the N-Myc target genes ODC1 and E2F2. DOT1L bound to the Myc Box II domain of N-Myc protein, and knocking down DOT1L reduced histone H3K79 methylation and N-Myc protein binding at the ODC1 and E2F2 gene promoters and reduced neuroblastoma cell proliferation. Treatment with the small molecule DOT1L inhibitor SGC0946 reduced H3K79 methylation and proliferation of MYCN gene-amplified neuroblastoma cells. In mice xenografted with neuroblastoma cells stably expressing doxycycline-inducible DOT1L small hair-pin RNA, ablating DOT1L expression with doxycycline significantly reduced ODC1 and E2F2 expression, reduced tumor progression and improved overall survival. In addition, high levels of DOT1L gene expression in human neuroblastoma tissues correlated with high levels of MYCN, ODC1 and E2F2 gene expression, and independently correlated with poor patient survival. Taken together, our data identify DOT1L as a novel co-factor in N-Myc-mediated transcriptional activation of target genes and neuroblastoma oncogenesis, and DOT1L inhibitors as novel anticancer agents against MYCN-amplified neuroblastoma.

Citation Format: Matthew Wong, Andrew Tee, Giorgio Milazzo, Jessica Bell, Stefan Hüttelmaier, Patsie Polly, Giovanni Perini, Christopher J. Scarlett, Tao Liu. The histone methyltransferase DOT1L promotes neuroblastoma by regulating gene transcription [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-080. doi:10.1158/1538-7445.AM2017-LB-080
Abstract LB-088: Role of histone demethylase JMJD1A in the generation of AR-V7
Authors: Fan Lingling , Zhang Fengbo , Gleave Martin , Dong Xuesen , Qi Jianfei
Published: July 2017

Formation of androgen receptor (AR) splicing variant, AR-V7, has been shown to contribute to the resistance of prostate cancer to androgen deprivation therapy and development of castration-resistant prostate cancer (CRPC). We and others have reported that histone demethylase JMJD1A promotes the transcriptional activity of AR by functioning as an AR co-activator. Here, we identified a new role for JMJD1A in the expression of AR-V7 in prostate cancer cells. Knockdown of JMJD1A reduced the mRNA and protein level of AR-V7 but had little effect on the full-length AR (AR-FL). Re-expression of AR-V7 in the JMJD1A-knockdown cells partly restored the expression of select AR target genes and growth of prostate cancer cells under the androgen deprivation condition in vitro and in the mouse xenograft model. Our preliminary data show that JMJD1A promotes the alternative splicing of AR-V7 and we are currently investigating the splicing factor(s) regulated by JMJD1A for the AR-V7 formation. Together, our data reveal that JMJD1A enhances the castration-resistant growth of prostate cancer cells by promoting the alternative splicing of AR-V7.

Note: This abstract was not presented at the meeting.

Citation Format: Lingling Fan, Fengbo Zhang, Martin Gleave, Xuesen Dong, Jianfei Qi. Role of histone demethylase JMJD1A in the generation of AR-V7 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-088. doi:10.1158/1538-7445.AM2017-LB-088
Abstract LB-090: p53 binding sites in normal and cancer-derived cells are characterized by distinct chromatin context
Authors: Cui Feng
Published: July 2017

The tumor suppressor protein p53 interacts with DNA in a sequence-dependent manner. Thousands of p53 binding sites have been mapped genome-wide in normal and cancer-derived cells. The way p53 selectively binds its cognate sites in different types of cells is not fully understood, however. We performed a comprehensive analysis of published p53 cistromes and identified 3,551 and 6,039 high-confidence normal and cancer binding sites that are enriched in genes involved in p53 signaling pathways. About 12% of these sites occur in the endogenous retrovirus 1 (ERV1) repeat family in the human genome. We further analyzed chromatin organization at the p53 binding sites in normal (GM12878) and cancer (K562) cells, and found that these sites are characterized by a high nucleosome occupancy and at the same time, by a high sensitivity to DNase I. Strikingly, compared to the sites derived from cancer cells, the p53 binding sites from normal cells are characterized by higher levels of transcriptionally active histone marks (H3K4me3 and H3K36me3) and DNA methylation. No difference was observed for the repressive histone marks (H3K27me3). These findings reveal two distinct epigenetic patterns associated with p53-DNA binding in normal and cancer-derived cells.

Citation Format: Feng Cui. p53 binding sites in normal and cancer-derived cells are characterized by distinct chromatin context [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-090. doi:10.1158/1538-7445.AM2017-LB-090
Abstract LB-091: CpG island DNA methylation regulates alternative cleavage and polyadenylation
Authors: Sweet Thomas , Jin Lihua , Dermawan Josephine , Ting Angela H.
Published: July 2017

Abnormal DNA methylation pattern is a hallmark of human cancer, and our work in genomic profiling of DNA methylation patterns in prostate and colon cancers have identified the majority of unique DNA hypermethylation to occur outside of gene promoters. While promoter hypermethylation causes transcriptional silencing, the functions of non-promoter DNA methylation are poorly defined. Thus, we began investigating the impact of non-promoter DNA methylation on the transcriptome and specifically focused on studying the functions of DNA methylation near gene 3' ends. Using a pair of isogenic cancer cells (HCT116 and DKO cells) that differ specifically in their ability to maintain DNA methylation, we discovered an intriguing association between gene 3' end differential DNA methylation and alternative cleavage and polyadenylation (APA) events. Briefly, pre-mRNAs undergo cleavage and polyadenylation as part of normal mRNA 3' end formation, and alternative sites of cleavage and polyadenylation can be utilized to produce transcripts with varying regulatory sequences in the 3' untranslated regions (3' UTRs) or protein isoforms via APA within coding sequences. Previous studies have demonstrated that cancer cells can hijack the APA pathway to skew expression of short 3' UTRs in oncogenes to evade negative regulation, highlighting APA as an important process involved in cancer initiation and progression. By using pharmacologic inhibition of DNA methylation and reporter constructs, we demonstrated that CpG island DNA methylation near polyadenylation sites is necessary and sufficient for determining relative usage, most likely by modulating RNA polymerase II elongation rate. By leveraging the Cancer Genome Atlas (TCGA) and the Roadmap Epigenomics data, we could observe the correlation between gene 3' DNA methylation and APA at select loci in vivo. The results of our study will improve overall functional understanding of non-promoter DNA methylation, provide a novel mechanism for APA regulation, and ultimately accelerate discovery of novel targets for cancer management.

Note: This abstract was not presented at the meeting.

Citation Format: Thomas Sweet, Lihua Jin, Josephine Dermawan, Angela H. Ting. CpG island DNA methylation regulates alternative cleavage and polyadenylation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-091. doi:10.1158/1538-7445.AM2017-LB-091
Abstract LB-092: High impact of methylation accumulation on cancer risk: 5-year follow-up of a multicenter prospective cohort study
Authors: Maeda Masahiro , Nakajima Takeshi , Oda Ichiro , Shimazu Taichi , Yamamichi Nobutake , Maekita Takao , Asada Kiyoshi , Yokoi Chizu , Ando Takayuki , Yoshida Takeichi , Nanjo Sohachi , Fujishiro Mitsuhiro , Gotoda Takuji , Ichinose Masao , Ushijima Toshikazu
Published: July 2017

Aberrant DNA methylation can be accumulated in normal-appearing tissues, and its degree can be correlated with cancer risk [Hattori, Genome Med, 8:10, 2016]. Such accumulation is especially prominent in inflammation-associated cancers, including gastric cancer. To bring the findings into cancer risk diagnosis, we conducted a multicenter prospective cohort study with 826 patients [Asada, Gut, 64:388, 2015].

Between 2008 and 2010, 826 patients after endoscopic treatment of gastric cancer and without current H. pylori infection were enrolled, and a gastric biopsy was collected. Methylation levels of pre-defined three marker genes (miR-124a-3, EMX1 and NKX6-1) were measured by quantitative methylation-specific PCR. Patients were classified into quartiles according to methylation levels of individual genes (Q1, the lowest; Q4, the highest).

Among the 826 enrolled patients, 795 patients received annual follow-ups by endoscopy with a median period of 5.46 years (interquartile range: 3.95 - 6.09). By the end, 133 patients developed a metachronous gastric cancer, and 116 of them developed a cancer after 1 year of the enrollment (authentic metachronous cancer). Kaplan-Meier analysis showed that Q4 had a higher cumulative incidence of metachronous gastric cancer than Q1 with p-values of <0.001 to 0.004 (log-rank test). Multivariate analyses adjusted for hospital, gender and age, pepsinogen index, history of endoscopic treatment, smoking and green vegetable intake also showed that Q4 had significantly high HRs compared with Q1, being 3.0 (95%CI: 1.58 to 5.72, p=0.0017) for miR-124a-3 [Maeda, Gut, online].

The results clearly showed that accumulation levels of aberrant DNA methylation can be used for cancer risk diagnosis. Even among the patients who carried a high risk of metachronous gastric cancer, cancer risk stratification was achieved. The strong influence of methylation accumulation on gastric cancer risk indicated a large contribution of aberrant DNA methylation to H. pylori infection-induced gastric carcinogenesis. Epigenetic cancer risk diagnosis is now becoming real.

Citation Format: Masahiro Maeda, Takeshi Nakajima, Ichiro Oda, Taichi Shimazu, Nobutake Yamamichi, Takao Maekita, Kiyoshi Asada, Chizu Yokoi, Takayuki Ando, Takeichi Yoshida, Sohachi Nanjo, Mitsuhiro Fujishiro, Takuji Gotoda, Masao Ichinose, Toshikazu Ushijima. High impact of methylation accumulation on cancer risk: 5-year follow-up of a multicenter prospective cohort study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-092. doi:10.1158/1538-7445.AM2017-LB-092
Abstract LB-113: Immune-mediated anti-tumor activity with a clinical stage BET bromodomain inhibitor ODM-207 in pre-clinical models
Authors: Deshpande Pratima , Babu Ravi Krishna , Vadnal Prashant Yallappa , Jaleel Mahaboobi , Ramachandra Murali , Abbineni Chandrasekhar , Samajdar Susanta , Moilanen Anu-Maarit , Kallio Pekka
Published: July 2017

Background: ODM-207 is a potent and selective BET inhibitor that is structurally unrelated to the benzodiazepine-based inhibitors including JQ1, I-BET762, and OTX015. Phase I clinical trials have now been initiated with this agent based on its potent anti-tumor activity in various in vitro and in vivo models of hematologic malignancies and solid tumors. In view of the recent publications implicating a role for BET protein BRD4 in the suppression of PD-L1 expression, an immune checkpoint ligand for PD-1, we sought to evaluate ODM-207 for its effect on immune-mediated anti-tumor efficacy in pre-clinical models.

Methods and Results: Mouse splenocytes were stimulated with anti-CD3 and anti-CD28 in the presence or absence of ODM-207 for four days and changes in immune cell population were analyzed by FACS. Results revealed an increase in the level of activated cytotoxic CD8+ T cells as indicated by increased intracellular IFNγ and granzyme B with ODM-207 treatment. After confirming the lack of direct anti-proliferative activity on the mouse colon carcinoma cell line CT26, in vivo evaluation of ODM-207 was carried out in the syngeneic CT26 subcutaneous tumor model established in BALB/c mice. Daily oral administration of ODM-207 at 30 mg/kg was well tolerated in this model and resulted in a statistically significant inhibition of tumor growth. Interestingly, the tumor growth inhibition observed with ODM-207 was comparable to that with a commercially available anti-mouse PD1 antibody. Studies to characterize the immune changes in the tumor and anti-tumor activity of ODM-207 in combination with an anti-mouse PD1 antibody are currently underway and the results will be presented.

Conclusions: In summary, these studies demonstrate the anti-tumor activity of BET inhibitor in a syngeneic model of colon carcinoma in the absence of a direct anti-proliferative activity on tumor cells. Observed tumor growth inhibition correlated with the in vitro activation of cytotoxic CD8+ T cells supporting the immune-mediated effect leading to tumor growth inhibition. In view of the remarkable success with the immune-based therapeutic approaches, these findings are relevant in devising appropriate strategies for the continued clinical development of ODM-207.

Citation Format: Pratima Deshpande, Ravi Krishna Babu, Prashant Yallappa Vadnal, Mahaboobi Jaleel, Murali Ramachandra, Chandrasekhar Abbineni, Susanta Samajdar, Anu-Maarit Moilanen, Pekka Kallio. Immune-mediated anti-tumor activity with a clinical stage BET bromodomain inhibitor ODM-207 in pre-clinical models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-113. doi:10.1158/1538-7445.AM2017-LB-113
Abstract LB-115: TPRKB dependency in p53-deficient cancers
Authors: VanDenBerg Kelly , Goswami Moloy , Wang Lei Lucy , Singh Bhavneet , Weiss Travis , Han Sumin , Rhodes Dan , Feng Felix , Tomlins Scott
Published: July 2017

TP53 (p53) is an extensively studied tumor suppressor mutated in approximately 50% of all cancers. Identification of vulnerabilities imposed by p53 alterations may enable effective targeted therapy development. Thus, this study aimed to identify and characterize novel vulnerabilities in this context. Through analyzing shRNA screening data from the Broad Institute’s Project Achilles, we identified TPRKB, a poorly characterized member of the tRNA-modifying EKC/KEOPS complex, as the most significant vulnerability in p53 mutated cancer cell lines. In vitro, across multiple benign-immortalized and cancer cell lines, we confirmed that TPRKB knockdown in p53-deficient cells significantly inhibited proliferation, while there was little to no effect in p53 wild-type cells. Furthermore, p53 reintroduction into TPRKB-sensitive p53-null cells resulted in loss of TPRKB sensitivity, confirming the importance of p53 status in this context. To determine whether this response was unique to TPRKB or a result of impairment of the EKC/KEOPS complex, we knocked down other members of the complex: PRPK, OSGEP, and LAGE3. PRPK loss showed minor changes between p53 wild type versus deficient cells; while OSGEP and LAGE3 loss resulted in a significant decrease regardless of p53 status. For the first time, we have demonstrated a potential role for TPRKB in cancer, and our results suggest that effects of TPRKB knockdown in p53-deficient cancer cells may be independent of its role in the EKC/KEOPS complex.

Citation Format: Kelly VanDenBerg, Moloy Goswami, Lei Lucy Wang, Bhavneet Singh, Travis Weiss, Sumin Han, Dan Rhodes, Felix Feng, Scott Tomlins. TPRKB dependency in p53-deficient cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-115. doi:10.1158/1538-7445.AM2017-LB-115
Abstract LB-121: ACK in BRAF inhibitor resistance
Authors: Ji Zhenyu , Tsao Hensin , Hannes Mikula , Njauw Jenny , Kumar Raj
Published: July 2017

BRAF inhibition by the small-molecule drug vemurafenib or dabrafenib achieves enormous success in the treatment of melanoma. However, melanoma patients lose their responsiveness after 6 months of treatment. Activation of receptor tyrosine kinase (RTK) was found in vemurafenib resistant melanomas and considered as a critical factor contributing to vemurafenib resistance. We hypothesize that the quick relapse after BRAFi therapy is at least partly due to the off targets of these drugs. Using trans-cyclooctene(TCO) moiety conjugated vemurafenib to treat melanoma cells in culture, we were able to confirm that ACK is a bona-fide intracellular target of vemurafenib. ACK, a protein kinase that regulates turnover of EGFR and other RTKs, was then identified to be downregulated in melanoma cells after short term vemurafenib treatment. Furthermore, ACK protein was reduced in multiple vemurafenib resistant melanoma cells. To prove ACK downregulation plays a role in vemurafenib resistance development, we knocked down ACK by shRNA. We found that ACK reduction delays EGFR degradation speed and increases EGFR protein expression. Since EGFR overexpression has been demonstrated as one important driver of vemurafenib resistance, we expected ACK reduction by shRNA would lead to BRAFi resistance, which was then confirmed by viability assay. During the development of BRAFi resistance, MITF is lost, which is accompanied by overexpression of growth factors and cytokines. We proved that higher resistance to vemurafenib can be induced by combination of ACK reduction and addition of EGFR ligands and cytokines. Our data suggest that EGFR activation in vemurafenib resistant melanoma is mediated by a combination of ACK and MITF downregulation, which lead to RTK and growth factor/cytokine upregulation. ACK binding and downregulation by BRAFi might be the first step toward resistance and a loophole inherent in these compounds themselves. Thus, optimizing BRAFi to ensure more selectivity should be a critical step further to improve the long-term benefits of this class of drugs.

Note: This abstract was not presented at the meeting.

Citation Format: Zhenyu Ji, Hensin Tsao, Mikula Hannes, Jenny Njauw, Raj Kumar. ACK in BRAF inhibitor resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-121. doi:10.1158/1538-7445.AM2017-LB-121
Abstract LB-123: Identification of the molecular mechanisms of resistance to NTRK inhibitors and the potential therapeutic strategies in NTRK1-rearranged cancers
Authors: Katayama Ryohei , Fuse Miho J. , Oh-hara Tomoko , Ogura Hayato , Fujita Naoya
Published: July 2017

Neurotrophic receptor tyrosine kinase 1 (NTRK1) gene rearrangement leads to constitutive activation of NTRK1, which induces high transforming ability. NTRK-rearranged cancers have been identified in several cancer types, such as glioblastoma, non-small-cell lung cancer, and colorectal cancer. Although there are currently no clinically available inhibitors that target NTRK1, several tyrosine kinase inhibitors (TKIs), such as entrectinib and LOXO-101, are in clinical trials. To identify potential mechanisms of resistance to NTRK inhibitors and find potential therapeutic strategies to overcome the resistance, we examined the sensitivity of TPM3-NTRK1-transformed Ba/F3 cells and TPM3-NTRK1-harboring KM12 cells to multiple NTRK inhibitors. Then, acquired NTRK inhibitor-resistant mutations were screened by N-ethyl-N-nitrosourea (ENU) mutagenesis with Ba/F3-TPM3-NTRK1 cells or by the establishment of NTRK-TKI-resistant cells from KM12 cells continuously treated with NTRK-TKIs. After identifying the resistance mechanisms, we performed drug screening with small-molecular inhibitors to overcome the resistance. As the results, we identified multiple novel NTRK-TKI resistance mutations in the NTRK1 kinase domain, including G595R. As a result of drug screening, we found that cabozantinib and a few TKIs effectively inhibited the survival of TPM3-NTRK1-G667C but not G595R mutants, both of which showed resistance to entrectinib or LOXO101. Furthermore, cabozantinib with an insulin growth factor receptor type 1 (IGF1R) inhibitor such as OSI906 could overcome bypass pathway-mediated resistance. Thus, in this study, we developed a comprehensive model of acquired resistance to NTRK inhibitors in cancer with NTRK1 rearrangement. In addition, we found drugs and a combination therapy to overcome the identified resistance to NTRK1-TKI.

Citation Format: Ryohei Katayama, Miho J. Fuse, Tomoko Oh-hara, Hayato Ogura, Naoya Fujita. Identification of the molecular mechanisms of resistance to NTRK inhibitors and the potential therapeutic strategies in NTRK1-rearranged cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-123. doi:10.1158/1538-7445.AM2017-LB-123
Abstract LB-124: COP1 E3 ligase modulates response to oncogenic MAPK pathway inhibition
Authors: Mayekar Manasi K. , Bivona Trever
Published: July 2017

Oncogenic activation of the RAS-MAPK pathway is the underlying cause of the majority of lung adenocarcinomas. In these tumors, RAS-MAPK pathway activation occurs via diverse genetic alterations in upstream receptor tyrosine kinases such as EGFR and ALK as well as in RAS, BRAF, MEK and RAS GTPase activating protein (GAP) and tumor suppressor, NF1. Therapies targeting components of the RAS-MAPK pathway can lead to initial tumor responses in many patients. But most patients show only a partial response and many do not respond at all despite the presence of a RAS-MAPK pathway-activating genetic lesion in the tumor. Hence, it is critical to understand the molecular basis of response and resistance to targeted therapies acting against the RAS-MAPK pathway in lung adenocarcinomas in order to improve patient survival. We conducted a genetic screen to identify modifiers of response to MAPK pathway inhibition in lung cancer. Our genetic screen uncovered the E3 ubiquitin ligase COP1/RFWD2 as a novel genetic modifier. We found that depletion of COP1 and members of its complex, as well proteasomal subunits, confers resistance to RAS-MAPK pathway inhibition in human lung adenocarcinoma cells with oncogenically-activated MAPK pathway. Since two critical MAPK pathway effectors c-Jun and ETV1 have been shown to be targets of COP1 E3 ligase complex-mediated proteosomal degradation, we tested if depletion of COP1 alters the levels of phosphorylated c-Jun and ETV1. Intriguingly, we did not observe a substantial impact of COP1 depletion on the levels of these effectors. Based on these observations, we hypothesize that depletion of COP1 confers resistance to MAPK pathway inhibition in RAS-MAPK pathway driven lung adenocarcinomas through accumulation of a novel protein substrate(s) that allows the survival and/or proliferation of these cells upon MAPK pathway inhibition. We will uncover the mechanism of resistance by identifying this substrate(s) of COP1 whose accumulation facilitates cell survival and/or proliferation upon MAPK pathway inhibition. This work will improve our understanding of the molecular basis of tumor cell resilience during initial treatment as well as of primary treatment resistance. Additionally, it could lead to identification of a novel biomarker for predicting response to MAPK pathway inhibitor therapy and a therapeutic target(s) that could be co-targeted with MAPK pathway signaling to improve the patient response in MAPK pathway driven lung adenocarcinomas.

Citation Format: Manasi K. Mayekar, Trever Bivona. COP1 E3 ligase modulates response to oncogenic MAPK pathway inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-124. doi:10.1158/1538-7445.AM2017-LB-124
Abstract LB-129: NDAT and P-bi-TAT formulations of tetraiodothyroacetic acid (tetrac) induce devascularization, necrosis and apoptosis in glioblastoma xenografts
Authors: Davis Paul J. , Thangirala Sudha , Sell Stewart , Hercbergs Aleck , Mousa Shaker A.
Published: July 2017

Thyroid hormone as L-thyroxine (T4) has been reported to stimulate proliferation of multiple glioma cell lines in vitro and there is clinical evidence that medical induction of hypothyroidism slows growth of glioblastoma multiforme (GBM). The proliferative action of T4 on glioma cells is initiated at a cell surface receptor for thyroid hormone on the extracellular domain of integrin αvβ3. Tetraiodothyroacetic acid (tetrac) is a thyroid hormone (T4) derivative that blocks T4 action at αvβ3 and has anticancer and anti-angiogenic activity. Tetrac has been covalently bonded via a linker to a nanoparticle (Nanotetrac, Nano-diamino-tetrac, NDAT) or to two polyethylene glycol (PEG) molecules (P-bi-TAT) that increase the potency of tetrac and broadens the anticancer properties of the drug. In the present studies of U87 MG GBM xenografts, NDAT administered daily for 10 days s.c. as 1 mg tetrac equivalent/kg reduced tumor xenograft weight at animal sacrifice by 50%, compared to untreated control lesions (p <0.01). Histopathological analysis of tumors revealed a 95% loss of the vascularity of treated tumors compared to controls at 10 days (p <0.001). There was no intratumoral hemorrhage. There was extensive cellular necrosis in treated tumors attributable to devascularization. Cells not necrotic in treated xenografts exhibited apoptosis, so that 80% of cells were either necrotic or apoptotic, compared to controls (p <0.001). Induction of apoptosis in cancer cells is a well-described quality of NDAT. P-bi-TAT treatment resulted in similar results after 20 days of treatment, but included a 21-day off-treatment follow-up after therapy. Xenografts achieved a 95% volume loss in the off-treatment, follow-up phase (P < 0.001). In summary, systemic NDAT and P-bi-TAT have been shown to be effective by multiple mechanisms in treatment of GBM xenografts.

Citation Format: Paul J. Davis, Sudha Thangirala, Stewart Sell, Aleck Hercbergs, Shaker A. Mousa. NDAT and P-bi-TAT formulations of tetraiodothyroacetic acid (tetrac) induce devascularization, necrosis and apoptosis in glioblastoma xenografts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-129. doi:10.1158/1538-7445.AM2017-LB-129
Abstract LB-136: Characterization of residual Basal Cell Carcinoma after vismodegib treatment
Authors: Biehs Brian , Dijkgraaf Gerrit J. , Alicke Bruno , Peale Franklin , Gould Stephen E. , Sauvage Frederic J. de
Published: July 2017

We have generated a mouse model of Superficial Basal Cell Carcinoma (BCC) to study the effect of the Smoothened inhibitor vismodegib in vivo. Despite the potency of vimodegib in blocking Hedgehog (Hh) signaling and efficacy in treatment of BCC, residual disease persists in the mouse model. To better understand the Biology of BCC and the potential mechanisms maintaining BCC during treatment, we profiled isolated untreated as well as residual tumors. We found that treated tumors change their transcriptional program to resemble the cells of skin and hair follicle structures like the Interfollicular Epidermis (IFE) and Isthmus, both of which harbor stem cell compartments. Consistent with these findings, residual disease lacks expression of epidermal differentiation markers and initiates growth upon cessation of treatment. While Wnt signaling is clearly required for BCC initiation in mouse models, we show that Wnt signaling is down-regulated in untreated full-blown disease and subsequently strongly induced in the treated tumors. We hypothesize that re-initiation of the Wnt pathway maintains BCC and study the effect of blocking both Wnt and Hh pathways with combined treatment of vismodegib and Wnt inhibitors.

Citation Format: Brian Biehs, Gerrit J. Dijkgraaf, Bruno Alicke, Franklin Peale, Stephen E. Gould, Frederic J. de Sauvage. Characterization of residual Basal Cell Carcinoma after vismodegib treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-136. doi:10.1158/1538-7445.AM2017-LB-136
Abstract LB-140: Inhibition of cancer stemness sensitizes colorectal cancer to immune checkpoint inhibitors
Authors: Gao Yuan , Li Youzhi , Hsu Eric , Wang Yuxin , Huang Janet , Brooks Emily , Li Chiang J.
Published: July 2017

Cancer stem cells (CSCs), a highly malignant tumor cell subpopulation capable of self-renewal, are considered to be fundamentally responsible for malignant growth and tumor recurrence. Emerging evidences indicate that CSCs and CSC pathways, such as STAT3, beta-Catenin, CD44 and Nanog pathway, are involved in the immune evasion in cancers. With the exception of a small percentage of colorectal cancers (CRC) patients that display microsatellite instability (MSI), the vast majority of CRC patients have been found to be resistant to immune checkpoint therapies. BBI-608 (napabucasin) is an orally-administered first-in-class cancer stemness inhibitor that works by targeting STAT3, which lead to inhibition of multiple cancer stemness pathways, including Stat3 and β-catenin pathways. In this study, we investigate the effect of cancer stemness inhibition on sensitizing CRC to immune checkpoint inhibitors in preclinical models. In the syngeneic tumor model, anti-PD-1 antibody monotherapy produced low level and temporary antitumor activity with rapid development of complete resistance to anti-PD1 in the MSS CT26 CRC model. The anti-PD-1 antibody treated CT26 tumors exhibited increased p-STAT3 activation and overexpression of a variety of stemness factors, including Nanog, CD44 and CD133, as well as enrichment of sphere-forming stemness-high cancer cells. BBI-608 was able to reduce basal as well as anti-PD1-induced STAT3 activation and other CSC features within CT26 tumors. Combination of stemness inhibitor BBI-608 with anti-PD-1 antibody to treat CT26 tumors led to tumor complete response (CR) virtually in all treated CT26 tumors with 40% of the mice remain tumor-free for 30 days following treatment termination. This combination also had a synergistic effect on the influx of tumor infiltrating CD8+ T cells, which likely contributed to the rapid tumor regression. Finally, mice CR-induced by BBI-608 and anti-PD-1 antibody were able to reject CT26 tumors upon rechallenge, but not the unrelated breast cancer 4T1 tumors. Our data suggests cancer stemness pathways contribute to immunotherapy resistance in MSS CRC and inhibition of cancer stemness by BBI-608 sensitizes colorectal cancer to immune checkpoint inhibition. This study provides compelling preclinical evidence to support the investigation of the combination of BBI608 with immune checkpoint inhibitors in CRC.

Citation Format: Yuan Gao, Youzhi Li, Eric Hsu, Yuxin Wang, Janet Huang, Emily Brooks, Chiang J. Li. Inhibition of cancer stemness sensitizes colorectal cancer to immune checkpoint inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-140. doi:10.1158/1538-7445.AM2017-LB-140
Abstract LB-149: ITGA1 marks pre-malignant pancreatic lesions and drives stem-like cell survival and TGFβ/collagen-induced therapy resistance and metastasis in pancreatic cancer
Authors: Kim Sa La , Gharibi Armen , Molnar Justin , Brambilla Daniel , Adamian Yvess , Hoover Malachia , Lin Joy , Hong Julie , Kelber Jonathan A.
Published: July 2017

Pancreatic ductal adenocarcinoma (PDAC) remains one of few malignancies to have single-digit 5-year survival rates at <7%. This dismal prognosis is due in part to the limited ability of clinicians to make pre-metastatic diagnoses and effectively treat localized pancreatic tumors. Thus, there is a dire need to improve early detection methods and identify new therapeutic targets for abrogating PDAC progression. To this end, we mined our previously published pseudopodium-enriched (PDE) protein/phosphoprotein datasets to identify novel PDAC-specific biomarkers and/or therapeutic targets. We discovered that 37 of the top 100 PDE proteins are frequently upregulated in human pancreatic cancer and other tumor types. Integrin alpha 1 (ITGA1) was of primary interest because its high expression in pancreatic cancer precursor lesions may provide a path toward earlier diagnoses, while targeting its cell surface function may abrogate tumor-stroma interactions known to exacerbate PDAC. In this regard, the expression of ITGA1-specific collagens within the pancreatic cancer microenvironment significantly correlates with indicators of poor patient prognosis such as high tumor grade, p53/SMAD4 mutation status and erlotinib resistance. Depleting ITGA1 from PDAC cells revealed that it is required for collagen-induced migration and survival. We further demonstrate that collagen induces PDAC cell attachment and spreading in an ITGA1-dependent manner. Notably, collagen/ITGA1 signaling promotes the survival of ALDH1-positive stem-like cells and cooperates with TGFβ to drive gemcitabine resistance. Finally, we report that increased ITGA1 expression in PDAC tissue indicates the presence of epithelial-mesenchymal transition (EMT) and that ITGA1 is required for TGFβ/collagen-induced EMT and hepatotropic metastasis. Our data suggest that ITGA1 is a new biomarker for PDAC initiation and, when targeted, can sensitize tumors to available chemotherapies to suppress the growth of pancreatic tumors at primary and metastatic sites.

Citation Format: Sa La Kim, Armen Gharibi, Justin Molnar, Daniel Brambilla, Yvess Adamian, Malachia Hoover, Joy Lin, Julie Hong, Jonathan A. Kelber. ITGA1 marks pre-malignant pancreatic lesions and drives stem-like cell survival and TGFβ/collagen-induced therapy resistance and metastasis in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-149. doi:10.1158/1538-7445.AM2017-LB-149
Abstract LB-154: Methylation profiling of ovarian cancer shows prognostic heterogeneity of histological subtypes and high-grade serous
Authors: Bodelon Clara
Published: July 2017

Background. Ovarian cancer is a heterogeneous disease that is divisible into multiple subtypes with variable pathogenesis, etiology and biological behavior. We analyzed DNA methylation profiling data to identify biologic subgroups of ovarian cancer and study their relationship with histologic subtypes and prognosis.

Methods. A total of 176 paraffin embedded ovarian epithelial tumor tissues, including the four major epithelial ovarian tumor subtypes (serous, endometrioid, mucinous and clear cell) and tumors of low malignant potential (LMP) were selected from two different sources: The Polish Ovarian Cancer study, an incident population-based case-control study conducted from 2001-2004, and the Surveillance, Epidemiology, and End Results Residual Tissue Repository (SEER RTR), which included ovarian tumors blocks collected between 1994 and 2004 from the Iowa and Hawaii SEER registries. The distributions of tumor histologic subtypes and grades from the studies were similar. All analyses were restricted to Caucasian women. Methylation profiling was conducted using the Illumina 450K methylation array. Analyses were restricted to the 22 autosomal chromosomes and non-SNP probes. Fourteen samples that did not pass quality control were excluded from the analysis.

Results. Among 162 samples, 32 were from the Polish study and 130 were from the SEER RTR. Unsupervised hierarchical clustering of the 5,000 most variable CpG sites showed 4 major clusters: Cluster 1 with 79% invasive serous and 14% endometrioid carcinomas, including the majority of high grade carcinomas; cluster 2 with 77% either endometrioid or clear cell carcinomas; cluster 3 with 71% serous LMP; and cluster 4 with 73% mucinous carcinomas. We observed significant survival differences across these clusters (long-rank test P= 4.27×10-6), similar to differences observed for histologic subtypes. Within high grade (HG) serous carcinomas, clustering showed three subgroups with prognostic significance (long-rank test P= 0.008).

Conclusions. Our results suggest that methylation-based subtypes provide a classification of ovarian tumors that are in agreement with morphologic subtypes and probable mechanisms of origin. Unsupervised clustering analysis of HG serous carcinomas showed subtypes within HG serous with significance survival difference. Ongoing analyses are comparing performance of the methylation subgroups with gene expression subgroups of ovarian cancer.

Citation Format: Clara Bodelon. Methylation profiling of ovarian cancer shows prognostic heterogeneity of histological subtypes and high-grade serous [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-154. doi:10.1158/1538-7445.AM2017-LB-154
Abstract LB-163: Biological differences underlying racial disparity in breast cancer
Authors: Shendre Aditi , Liu Yunlong , Storniolo Anna Maria , Schneider Bryan P. , Han Jiali , He Chunyan
Published: July 2017

Compared to European American (EA) women, African American (AA) women have higher rates of estrogen receptor negative (ER-) breast cancer, more specifically triple-negative (TN) subtype, and show poorer prognosis and survival. Increasing evidence suggests biological differences may contribute to the observed racial disparity. Studies evaluating racial differences in gene expression in breast tumor tissue have reported inconsistent results. Study of normal breast tissue in healthy women may provide new insight into biological mechanisms for cancer development prospectively before tumor occurrence. However, racial influence on gene expression in normal breast tissue has not been extensively studied. In this study, we evaluated racial differences in gene expression in normal breast tissue obtained from 23 healthy women as well as tumor tissue obtained from 108 breast cancer patients. We analyzed RNA-sequencing data and performed differential expression analysis between AA and EA women. We found that differentially expressed genes in normal breast tissue between AA and EA women were enriched in biological pathways related to amino acid metabolism, immune response and signaling, lipid and protein biosynthesis, and cell proliferation and survival. Many of these biological differences persist in tumor tissue between EA and AA women in a subtype-specific manner. For example, in ER- breast cancer, racial differences in gene expression were enriched in amino acid metabolism, cell proliferation and survival pathways, with particular enrichment in immune response and signaling and lipid metabolism pathways in TN breast cancer. For ER+ breast cancer, we did not find any major biological pathway enrichment. In addition, we identified several microRNAs differentially expressed in normal breast tissue between EA and AA women. They may be involved in racial differences in breast carcinogenesis but their potential downstream effects are yet to be determined. Future studies are needed to validate our findings and understand racial-specific biological mechanisms in breast cancer development.

Citation Format: Aditi Shendre, Yunlong Liu, Anna Maria Storniolo, Bryan P. Schneider, Jiali Han, Chunyan He. Biological differences underlying racial disparity in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-163. doi:10.1158/1538-7445.AM2017-LB-163