bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4018: Identifying allosteric modulators of KRas using second harmonic generation
Authors: Vo Elizabeth Donohue , Mercado Gabriel Besserer , Alexander Patrick , Moree Ben , Van Que , Stephen Andrew G. , Salafsky Joshua , McCormick Frank 
Published: July 2017

Abstract
The Ras protein family consists of small GTPases that are critical signaling transducers regulating cellular processes including proliferation, differentiation, and survival. As monomeric GTPases, Ras proteins cycle between an inactive GDP-bound state and an active GTP-bound state. Oncogenic mutations in one of the Ras isoforms, H-, N-, and K-Ras, impair GTP hydrolysis, thus de-regulating Ras signaling. Ras mutations are found in one-third of human cancers, and tumors bearing these mutations are notoriously difficult to treat. Conventional approaches to inhibit Ras with small molecules have been largely unsuccessful leading many to characterize the Ras family as an “undruggable” target. However, there is renewed enthusiasm towards Ras drug discovery in response to a recent surge of reports revealing structural complexities to Ras proteins that provide opportunity for innovative drug discovery efforts.
In light of findings suggesting KRas contains transient and dynamic binding pockets, many of which are undetectable with traditional structural techniques, we used a second harmonic generation (SHG) platform to screen a ~2700 chemically diverse fragment collection for allosteric modulators of KRas. This high throughput SHG platform enables real-time measurement of protein conformational change under physiological conditions. We selected ~50 fragments for validation by SPR, and positive binders will be selected for structural and biochemical characterization. Another advantage of the SHG platform is that we can monitor the conformational dynamics of fully processed, farnesylated KRas bound to a phosphatidylserine-enriched membrane that mimics KRas’ physiological interaction with the plasma membrane. No other biophysical method is suitable to monitor the real-time interactions of small molecules or proteins with membrane-bound KRas. This analysis may reveal surface contacts unavailable in solution-based assays. We have successfully implemented SHG as a drug discovery platform against KRas, and we aim to utilize selected KRas conformational modulators towards the identification of novel binding pockets and towards the development of targeted KRas therapies.
Citation Format: Elizabeth Donohue Vo, Gabriel Besserer Mercado, Patrick Alexander, Ben Moree, Que Van, Andrew G. Stephen, Joshua Salafsky, Frank McCormick. Identifying allosteric modulators of KRas using second harmonic generation [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 4018. doi:10.1158/1538-7445.AM2017-4018
Abstract 4030: Celsee™ SingleCell Chip can retrieve rare single cells with 100% efficiency for genetic analysis
Authors: Handique Kalyan , Gogoi Priya , Chow William , Gleason Kyle , Payne Auston , Sharma Vishal Premdev , Wang Yixin 
Published: July 2017

Abstract
Tumors are comprised of heterogeneous cells. Only a specific or rare population of tumor cells is capable of metastasizing through blood. While mapping out the genome of cancer cells, gene expression variations indicative of more aggressive cancer cells might be missed among the noise. Therefore, single cell gene expression and mutation analysis provide a more comprehensive and most precise information about the heterogeneity of cancer progression and metastasis. Although there has been a surge in technologies used for selection and analysis of single cells, single cell analysis of rare cells such as circulating tumor cells (CTCs) is fraught with technical challenges. Among many used techniques to isolate single cells, the most common cell separation method is cell sorting by flow cytometry, which requires cell labeling. The numerous steps involved in cell labelling and centrifugation result in significant cell loss and changes in gene expression. In addition, centrifugation may also cause shear-induced gene expression changes in viable cells. For other single cell analysis platforms, there is a minimum input of cells ranging from 200 - 1000 cells. Rare cells like CTCs are found in the range of 1-10 per mL of blood. Another challenge is that the input volume required for these systems is very low usually in microliters. Here, we introduce a novel microfluidic chip with 250,000 microwells which captures cells at 100% efficiency down to one cell with a dynamic range over 5 logs. The underlying principle of this technology is that the geometric pattern of the microfluidic chip captures a single cell from an initial volume of up to 1 mL of fluid due to cell settling. The unique microwell structure promotes easy fluid exchange without perturbing the cells from their captured locations, thereby eliminating cell loss during multistep downstream processing. Preliminary tests have shown that single or cluster of spiked cancer cells in blood can be immunostained, both live or fixed and can also be retrieved very efficiently from this chip using a micro capillary. The retrieved single cells can further be used for several single cell genetic analysis. We will present data describing cancer gene expression and gene mutation analysis in isolated single cells.
Citation Format: Kalyan Handique, Priya Gogoi, William Chow, Kyle Gleason, Auston Payne, Vishal Premdev Sharma, Yixin Wang. Celsee™ SingleCell Chip can retrieve rare single cells with 100% efficiency for genetic analysis [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 4030. doi:10.1158/1538-7445.AM2017-4030
Abstract 4036: Induction of detrimental aneuploidy in basal breast cancer cells treated by MPS1 inhibitors in combination with paclitaxel
Authors: Anderhub Simon J. , Mak Grace WY , Faisal Amir , Walsh Katie , Gurden Mark , Day Liz , Innocenti Paolo , Woodward Hannah L. , Westwood Isaac M. , Cheung Kwai-Ming J. , Naud Sebastien , Hayes Angela , Box Gary , Brandon Alexis de Haven , Valenti Melanie R. , O’Fee Lisa , Saville Harry , Burke Rosemary , Montfort Rob LM van , Raynaud Florence I. , Eccles Suzanne A. , Blagg Julian , Hoelder Swen , Linardopoulos Spiros 
Published: July 2017

Abstract
Basal-like breast cancer has received considerable attention in recent years, but despite all efforts, conventional chemotherapy remains the main therapeutic option in the clinic with taxane therapy, the most frequently prescribed treatment. A significant reason for the lack of effective therapeutics may be related to the high degree of heterogeneity and aneuploidy which is characteristic for basal-like breast cancer. A new approach in this field is the concept that cancer cells may be targeted by the introduction of a detrimental level of aneuploidy. Inhibition of one of the main spindle assembly checkpoint kinases, MPS1 is a rational choice to achieve this goal. We report here the identification of a synergistic effect between the novel, oral, highly potent and selective MPS1 inhibitor CCT289346 and paclitaxel. We demonstrate robust synergism in multiple basal-like breast cancer cell lines and provide mechanistic insights into how both compounds’ individual properties work together to maximise mitotic defects thereby increasing aneuploidy and cell death in a single round of mitosis. Additionally, in vivo studies in basal-like breast cancer xenograft models, including patient derived xenografts and systemic metastatic models, using clinically relevant doses of paclitaxel with well-tolerated doses of CCT289346, demonstrate significant benefit of combination of the two agents in comparison to paclitaxel alone.
Citation Format: Simon J. Anderhub, Grace WY Mak, Amir Faisal, Katie Walsh, Mark Gurden, Liz Day, Paolo Innocenti, Hannah L. Woodward, Isaac M. Westwood, Kwai-Ming J. Cheung, Sebastien Naud, Angela Hayes, Gary Box, Alexis de Haven Brandon, Melanie R. Valenti, Lisa O’Fee, Harry Saville, Rosemary Burke, Rob LM van Montfort, Florence I. Raynaud, Suzanne A. Eccles, Julian Blagg, Swen Hoelder, Spiros Linardopoulos. Induction of detrimental aneuploidy in basal breast cancer cells treated by MPS1 inhibitors in combination with paclitaxel [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 4036. doi:10.1158/1538-7445.AM2017-4036
Abstract 404: A bi-clustering based computational approach to identify molecular markers for Neoadjuvant chemotherapy outcome prediction in complement to cancer subtype classifications
Authors: Zhang Chi , Liang Sen 
Published: July 2017

Abstract
Molecular stratification models have been well established for most cancer types to classify tumors into sub-types by using genome level molecular characteristics. Tumors of certain sub-type have distinct response to specific therapies. Hence a reliable molecular classification model can be applied to determine treatment strategy. Recent neoadjuvant chemotherapy, immunotherapies and gene targeted drugs and their possible combinations raise a demand for small subsets of novel molecular markers for outcome prediction in addition to the complete molecular profile based classification. However, it is unknown what genes have predictive power for a certain therapeutic strategy while the highly crossed clinical features increase the difficult to determine sample groups for marker identification that form a bi-clustering problem. In addition, predictive maker may be varied among different cancer sub-types. In this work, we developed a bi-clustering based computational framework to identify transcriptomic markers for predicting the outcome of neoadjuvant chemotherapy and adjuvant chemotherapy. Our computational approach identifies functional related gene expression modules show significant expression patterns in a subset of samples that are highly associated with one or several disease sub-types and with high predictive power for the outcome of certain. By applying the analysis to 8 breast carcinoma, 10 colorectal carcinoma and 3 acute myeloid leukemia data sets in public domain, we have identified sets of gene markers with high predictive power for chemotherapy outcome complementary to the existing molecular classifications, suggesting the bi-clustering based approach can improve the whole genome level molecular classification based outcome prediction.
Citation Format: Chi Zhang, Sen Liang. A bi-clustering based computational approach to identify molecular markers for Neoadjuvant chemotherapy outcome prediction in complement to cancer subtype classifications [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 404. doi:10.1158/1538-7445.AM2017-404
Abstract 4040: Short-term romidepsin treatment combined with clotrimazole or bifonazole leads to decreased mitochondrial hexokinase 2 and apoptosis in cancer cells
Authors: Robey Robert W. , McDonald Andrew J. , Kozlowski Hanna , Gottesman Michael M. , Bates Susan E. 
Published: July 2017

Abstract
In light of disappointing clinical trials in solid tumors, we have sought novel combinations to increase the efficacy of the histone deacetylase inhibitor (HDI) romidepsin. Hexokinase 2 (HK2) expression is increased in cancer cells and is postulated to prevent Bax-mediated cytochrome c release from mitochondria. Since romidepsin treatment induces apoptosis via the mitochondrial pathway, combining romidepsin with agents that detach mitochondrial HK2 might result in synergistic apoptotic effects. HCT-116 colon carcinoma cells were treated with 25 ng/ml romidepsin alone for 6h, or with romidepsin in the presence of 25 µM clotrimazole or bifonazole, compounds known to detach mitochondrial HK2. The medium was removed and cells were treated for an additional 42 h with or without clotrimazole or bifonazole. Cells were also treated with clotrimazole or bifonazole alone for 48 h. Apoptosis was then quantitated by annexin staining. While short-term romidepsin treatment alone induced modest annexin staining and 25 µM clotrimazole or bifonazole had little effect, the combination resulted in significant apoptosis. Similar effects were observed for A549 lung cancer cells, MDA-MB-231 breast cancer cells and 786-0 renal carcinoma cells. We also treated HCT-116 and A549 cells lacking Bak, Bax or both with the clotrimazole/romidepsin combination. Apoptosis was slightly increased in Bak-/- cells, reduced in Bax-/- cells and nearly completely abrogated in cells lacking both proteins compared to wild-type cells suggesting apoptosis occurred through the intrinsic pathway. The clotrimazole analog TRAM-34 was similarly active to clotrimazole. Protein expression was determined in cytoplasmic and mitochondrial fractions of cells treated with romidepsin, clotrimazole or both and we found a &gt;60% decrease in mitochondrial HK2 in cells treated with the combination versus untreated cells. Our results suggest that combining romidepsin with a compound that leads to decreased mitochondrial hexokinase, such as clotrimazole or bifonazole, results in increased apoptosis. We postulate that cell death following combined romidepsin and clotrimazole treatment requires an intact intrinsic apoptotic pathway and that HK2 serves an anti-apoptotic function at the mitochondria.
Citation Format: Robert W. Robey, Andrew J. McDonald, Hanna Kozlowski, Michael M. Gottesman, Susan E. Bates. Short-term romidepsin treatment combined with clotrimazole or bifonazole leads to decreased mitochondrial hexokinase 2 and apoptosis in cancer cells [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 4040. doi:10.1158/1538-7445.AM2017-4040
Abstract 4042: N-121, a novel polypeptide conjugate of SN-38, demonstrated enhanced intratumoral accumulation and sustained release of free SN-38 with potent antitumor activity
Authors: Wang Haojun , Li Wei , Zhou Xiaojian , Wan Liuyi , Wen Guanghui 
Published: July 2017

Abstract
Introduction: SN-38 is a critical chemotherapeutic agent active against a variety of solid tumors including advanced colorectal cancer. Clinical use of SN-38 is hampered by its poor solubility in pharmaceutically acceptable solvents. Although irinotecan, the only approved prodrug of SN-38, is widely used, its efficacy is limited by low conversion to the active SN-38 as well as hematologic and gastrointestinal dose-limiting toxicities. In an attempt to improve the water solubility, antitumor activity and safety profiles of SN-38, we synthesized a water soluble polypeptide-SN-38 conjugate (N-121) and examined its antitumor activity and pharmacokinetics (PK) in mouse models.
Methods: Antitumor activity and PK of SN-38, administered as N-121 or irinotecan, was evaluated following tail vein injection in male nude mice with subcutaneous orthotopic xenografts of the HCT116 human colon cancer. Mice received N-121 400 mgk (mg/kg) (32 mkg of eq. SN-38) or irinotecan 80 mgk once a week for 2 weeks and were followed for up to 46 days.
Results: N-121 drastically improved by over 1000 fold the water solubility of SN-38. At a SN-38 equivalent dose of less than half of that of irinotecan, N-121 resulted in a much longer tumor growth delay (36 days) than irinotecan (14 days). The more durable tumor growth inhibition with N-121 was consistent with its enhanced intratumoral accumulation: intratumoral trough levels of SN-38 were about 250-fold higher than those observed in plasma, compared with only 15-fold with irinotecan. With N-121, Intratumoral levels of SN-38 remained stable over the PK observation period (48 h), contrasting to a marked decline in SN-38 levels with irinotecan; intratumoral trough levels of SN-38 from N-121 were about 50-fold higher than those achieved with irinotecan. N-121 was well tolerated with a slight weight loss of 7.2%.
Conclusion: N-121, a novel water soluble polypeptide-SN-38 conjugate, exhibited enhanced and sustained intratumoral exposure of SN-38 with high antitumor activity in a mouse xenograft tumor model. These promising results warrant further evaluation of N-121.
Note: This abstract was not presented at the meeting.
Citation Format: Haojun Wang, Wei Li, Xiaojian Zhou, Liuyi Wan, Guanghui Wen. N-121, a novel polypeptide conjugate of SN-38, demonstrated enhanced intratumoral accumulation and sustained release of free SN-38 with potent antitumor activity [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 4042. doi:10.1158/1538-7445.AM2017-4042
Abstract 407: Whole-genome pooled CRISPR/Cas library screens to identify new hepatocellular carcinoma drivers and drug targets in combination with sorafenib
Authors: Kodama Takahiro , Newberg Justin Y. , Jenkins Nancy A. , Takehara Tetsuo , Copeland Neal G. 
Published: July 2017

Abstract
Backgrounds and Aims: Hepatocellular carcinoma (HCC) is a deadly cancer and its mortality rate ranks third among all cancer types worldwide. To comprehensively understand its genetic drivers, over 500 HCC genomes have been sequenced but they reveal the existence of thousands of infrequently mutated genes. This intra- and inter-tumor heterogeneity, combined with large number of passenger mutations, has made it difficult to identify the true drivers of HCC. In addition, sorafenib is the currently only FDA-approved molecular target drug in HCC but its anti-tumor effect is very limited. To overcome these problems, we performed two forward genetic screens using recently innovated whole-genome pooled CRISPR/Cas library. Methods: Two human liver cancer cell lines, Huh-7 and SNU-398, were lentivirally transduced with Geckov2 library and transduced cells were selected with puromycin. First, transduced cells were orthotopically injected into the liver of the Nude mice and monitored for tumor formation. To identify potential tumor suppressor genes (TSGs) in the liver, gRNAs enriched in the orthotopic liver tumors were determined by sequencing of gDNA in these tumors. Next, transduced cells were treated with vehicle or sorafenib in vitro for 14 days. To identify potential targets which inhibition show synergistic anti-tumor effect with sorafenib, we determined gRNAs depleted in cells with sorafenib treatment compared to cells with vehicle treatment. Results: In the first in vivo screening, we identified 62 genes targeted by 2 or more highly enriched gRNAs in Huh-7 cells-derived tumors and 47 genes in SNU-398 cells-derived tumors. Twenty-nine genes were common including 4 miRNAs. TCGA analysis revealed that HCC patients with mutation or copy number alteration in any of these genes showed worse overall survival and disease free survival compared to HCC patients without them. In addition, gene expression levels of 3 candidate TSGs, BPHL, CTSZ and PLCG2 were significantly negatively correlated with poor survival of HCC patients. In the second in vitro screening, CYP7B1, HS3ST5, NLRC4, and Mir-1237 were identified as potential drug targets in combination with sorafenib in HCC. Conclusion: Whole-genome pooled CRISPR/Cas library screens discovered potential new hepatocellular carcinoma drivers and drug targets in combination with sorafenib.
Citation Format: Takahiro Kodama, Justin Y. Newberg, Nancy A. Jenkins, Tetsuo Takehara, Neal G. Copeland. Whole-genome pooled CRISPR/Cas library screens to identify new hepatocellular carcinoma drivers and drug targets in combination with sorafenib [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 407. doi:10.1158/1538-7445.AM2017-407
Abstract 4080: Cytochrome P450 enzyme activity is enhanced in hepatocytes grown using a perfused 3D cell culture drug screening system
Authors: Shoemaker James T. , Vukasinovic Jelena 
Published: July 2017

Abstract
A critical requirement for assessing drug toxicity in vitro is cytochrome P450 (CYP) function that is physiologically representative. Due to low levels of CYP enzyme activity, cell lines such as HepG2 hepatocytes have largely been supplanted with primary cells derived from human donor tissue. While these cells retain CYP activity ex vivo, drug screening is limited to short-term assessments due to de-differentiation. This limits their efficacy in testing slow-clearing, large-molecule compounds such as antibody-based therapies and low-turnover drugs. Cell lines in monolayer cultures have been effective in assessing the safety of small molecule drugs, but the disparity between cell lines and in vivo tissue biology proves too substantial for current potential therapies. Three-dimensional (3D) cultures have been shown to be more physiologically relevant models of in vivo tissue. However, even they fail to fully mimic living tissue and suffer from the lack of active oxygen and nutrient transport. Lena Biosciences has developed a groundbreaking in vitro system that facilitates long-term survival of 3D cultures. Cells seeded in 3D hydrogels supported by a rigid scaffold are maintained in statistically independent wells in their own medium which floats atop a high-density blood-substitute in which medium is immiscible. Infusion and withdrawal of this blood-substitute introduces perfusion into a medium-throughput multiwell system without the need for separate pumps for each culture condition.
Internal validation experiments using hepatocytes cultured in a 12-well system showed a two-fold improvement in cellular respiration (measured by alamarBlue assay) over cultures maintained in a standard multiwell plate when the blood-substitute was introduced, and a three-fold improvement when the cultures were perfused. Cell viability (measured by LDH release) was significantly improved when perfusion was introduced. CYP activity (assessed using both fluorescent and luminescent substrate-based assays) was also significantly higher in the perfused hepatocyte cultures. These data demonstrate the substantial advantages to growing cells in this novel perfused cell culture model. Scaling the system to include multiple cell types (primary or cell lines), would allow for simultaneous testing of target and off-target effects of potential small or large molecule therapies. Thus, this system serves as a major improvement over the current organ-on-a-chip solutions in the area of drug safety testing.
Citation Format: James T. Shoemaker, Jelena Vukasinovic. Cytochrome P450 enzyme activity is enhanced in hepatocytes grown using a perfused 3D cell culture drug screening system [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 4080. doi:10.1158/1538-7445.AM2017-4080