bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract A16: Smad4 pathways modulate induction of the chemokine Ccl20 and repress inflammation-induced carcinogenesis in mouse colon
Authors: Means Anna L. , Freeman Tanner J. , Weaver Connie J. , Shi Chanjuan , Washington Mary K. , Wessinger Bronson C. , Brown Tasia , Flaherty David K. , Weller Kevin P. , Coffey Robert J. , Wilson Keith T. , Beauchamp Robert D.
Published: March 2017

Inflammation regulates many aspects of gut homeostasis but is also a key component of colon cancer progression. While TGFβ signaling is known to regulate inflammatory responses within immune cells, we have uncovered a novel regulatory pathway in which TGFβ and BMP signaling suppress responses to inflammatory stimuli within the colonic epithelium. Using mice with conditional deletion of Smad4 in intestinal epithelium, we found that CCL20 expression was increased with Smad4 loss. Similarly, in murine immortalized colonocytes and human colon cancer cell lines, blocking TGFβ and/or BMP receptors increased CCL20 expression. CCL20 is upregulated in response to inflammatory signals such as TNF and IL-1β. CCL20 is also upregulated in colon cancer but the mechanism is not understood. We found that pre-treatment of colonocytes or colon cancer cells with TGFβ1 and BMP2 completely suppressed TNF- or IL-1β-induced CCL20 expression at the level of gene transcription. By chromatin immunoprecipitation, we found that TGFβ1/BMP2 treatment impaired binding of NFκB and phospho-STAT3 to the CCL20 promoter. To understand the significance of this regulation in chronic inflammation, we subjected Smad4 deleted and control mice to three rounds of dextran sodium sulfate (DSS)-mediated damage to the distal colon. We found that loss of Smad4 in mouse colonic epithelium was sufficient to induce tumorigenesis following damage-induced inflammation. Following DSS-mediated damage, Smad4-null epithelium developed invasive colorectal adenocarcinoma within two months of DSS treatment while Smad4+ control mice never develop tumors following DSS exposure. The Smad4 null tumors were histologically similar to those of human colitis-associated colon cancers. Prior to tumor formation, we saw an increase in CD8+ cells in Smad4-deleted colons, suggesting that tumor progression involves bidirectional crosstalk between the epithelium and immune cells and that this crosstalk is regulated in part by Smad4-mediated signaling within the epithelium. SMAD4, TGFβ receptors, or BMP receptors are often mutated in colon cancer. This loss of TGFβ and/or BMP signaling likely facilitates epithelial-immune cell crosstalk in colitis-associated colon cancers.

Citation Format: Anna L. Means, Tanner J. Freeman, Connie J. Weaver, Chanjuan Shi, Mary K. Washington, Bronson C. Wessinger, Tasia Brown, David K. Flaherty, Kevin P. Weller, Robert J. Coffey, Keith T. Wilson, Robert D. Beauchamp. Smad4 pathways modulate induction of the chemokine Ccl20 and repress inflammation-induced carcinogenesis in mouse colon. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr A16.
Abstract A30: Novel non-COX inhibitory sulindac derivative with PDE10 inhibitory activity reduces incidence and multiplicity of colorectal adenomas in the APC+/min-FCCC mouse model
Authors: Lee Kevin J. , Chen Xi , Valiyaveettil Jacob , Lindsey Ashley S. , Andrews Joel , Ramirez-Alcantara Veronica , Keeton Adam B. , Piazza Gary A. , Clapper Margie L. , Chang Wen-Chi L.
Published: March 2017

Sulindac has been reported to reduce the number and size of precancerous colonic adenomas in patients with familial adenomatous polyposis (FAP), but is not recommended for long-term use as a cancer chemopreventive drug because of potentially fatal toxicities associated with cyclooxygenase (COX) inhibition. We report here a novel sulindac derivative, ADT-061, that lacks COX-1 and COX-2 inhibitory activity, yet potently and selectively inhibits colon tumor cells with IC50 values of 0.3-0.5 μM with no significant effect on the growth of normal colonocytes. By comparison, sulindac sulfide inhibits colon tumor cell growth with IC50 values of 40-60 μM, and has only modest tumor cell selectivity. ADT-061 inhibits phosphodiesterase 10A (PDE10), which increases intracellular cGMP levels, thus activates protein kinase G, suppresses nuclear levels of β-catenin, and induces cell cycle arrest and apoptosis, all within the same concentration range that inhibits tumor cell growth. ADT-061was evaluated for chemopreventive activity in the APC+/min-FCCC mouse model of colon cancer, which harbors colorectal adenomas that express PDE10. Colonoscopy exams were initially performed on all mice to ensure the absence of colorectal adenomas prior to treatment. At 7-8 weeks of age, male mice were treated with ADT-061 (1000ppm and 1500ppm) in the diet for 14 weeks. ADT-061 reduced the incidence of colorectal adenomas from 95.8% in the control group to 73.9% in the 1000ppm group (p=0.048), and 59.1% (p=0.004) in the 1500ppm group. Control untreated mice had an average of 2.98 colorectal adenomas per mouse, while mice treated with 1000ppm and 1500ppm ADT-061 had an average of 2.04 (p=0.102) and 1.91 (p=0.039) adenomas per mouse, respectively. These observations suggest that ADT-061, or analogs thereof, merit further drug development efforts for colorectal cancer chemoprevention.

Citation Format: Kevin J. Lee, Xi Chen, Jacob Valiyaveettil, Ashley S. Lindsey, Joel Andrews, Veronica Ramirez-Alcantara, Adam B. Keeton, Gary A. Piazza, Margie L. Clapper, Wen-Chi L. Chang. Novel non-COX inhibitory sulindac derivative with PDE10 inhibitory activity reduces incidence and multiplicity of colorectal adenomas in the APC+/min-FCCC mouse model. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr A30.
Abstract B14: TP53 synthetic lethal targets in colon cancer
Authors: Weige Charles C. , Liu Changlong , Anderson Erin L. , Banister Carolyn E. , Richardson Joseph , Contreras Carlo , Buckhaults Phillip J.
Published: March 2017

We have performed a genome-wide screen for pathways that are synthetic lethal with TP53 mutations in colon cancer. RKO colon cancer cells are wild type for TP53, and display robust p53-dependent growth arrest and apoptosis. We utilized an isogenic pair of RKO cells differing only in TP53 gene status (wild type vs homozygous null derivative) to screen a genome-wide GeCKO CRISPR library. After infection of these cells with the library and culturing for one week in vitro, we performed deep amplicon sequencing to identify CRISPR guide RNAs that were underrepresented in TP53 knockout cells. Multiple CRISPR guide RNAs targeting the CHEK1 and SHH genes were underrepresented in TP53 knockout cells. To validate these targets, we used CRISPR genome engineering to create an independent panel of six RKO clones with biallelic disruption of TP53, and tested small molecule inhibitors of CHEK1 (UCN01) and the SHH receptor SMO (Cyclopamine). TP53 null cells were tenfold more sensitive to UCN01, and 100-fold more sensitive to Cyclopamine, compared to TP53 wild type cells. Finally, the relevance of these findings to human colon cancers was confirmed by the establishment and treatment of colon cancer organoid avatars with either wild type or mutant TP53. Normal colon organoids, and tumor organoids with wild type TP53 were unaffected by either drug, whereas TP53 mutant organoids were significantly growth inhibited. Future studies will focus on testing these and additional targets, alone and in combination, against primary colon tumor and normal avatars and other preclinical models of TP53-mutant colon cancer.

Citation Format: Charles C. Weige, Changlong Liu, Erin L. Anderson, Carolyn E. Banister, Joseph Richardson, Carlo Contreras, Phillip J. Buckhaults. TP53 synthetic lethal targets in colon cancer. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr B14.
Abstract B19: Disruption of energy homeostasis as an approach to block the proliferation of colon carcinomatosis
Authors: Bozzi Fabio , Mogavero Angela , Varinelli Luca , Gloghini Annunziata , Leoni Valerio , Beznoussenko Galina V. , Mironov Alexandre A. , Leo Ermanno , Pierotti Marco A. , Bongarzone Italia , Gariboldi Manuela
Published: March 2017

Strategies aimed at obtaining a complete cytoreduction are needed to improve long-term survival for patients with colorectal cancer peritoneal carcinomatosis (CRC-pc). We established organoid models that presented cancer stem cell characteristics from naïve CRC-pc surgical samples of two patients (C1 and C2). The organoids recapitulated their corresponding clinical samples in terms of 3D structure and immmunoistochemical profile and were enriched in LGR5 positive cancer stem cells. Proteomic analyses of organoids highlighted their strong dependence on energy producing pathways, suggesting that their targeting may be an effective therapeutic approach for the ablation of cancer cell malignancies. To test this hypothesis we treated organoids with an inhibitor of MIF/CD74 signaling axis, 4-iodo-6-phenylpyrimidine (4-IPP), and metformin, which inhibits mitochondrial oxidation. Both the drugs target metabolism acting on AMP-activated protein kinase (AMPK), the main regulator of cellular energy homeostasis. AMPK inhibits the major anabolic processes sustaining cancer cell proliferation and growth and confers cell plasticity to survive under conditions of metabolic stress, such as hypoxia and glucose deprivation, which is commonly observed in tumors with rapid growth. As a new finding we observed that treatment of organoids with 4-IPP resulted in decreased AMPK signaling activity, inducing a stress-signaling response and death of cultured organoids. Conversely, metformin treatment enhanced AMPK activation under energy stress, decreasing the activity of the anabolic factors ribosomal protein S6 and p4EBP-1 and inhibiting the mitochondrial activity, hindering cell proliferation. Furthermore, metformin treated organoids exhibited a Warburg-like metabolic profile. Our results show that organoid metabolism can be disrupted by metformin-induced AMPK activation but also through a strong reduction in AMPK functions caused by the removal of MIF/CD74 signaling axis that induces an irreversible disruption of energy homeostasis and ultimately causes cell death. Overall, we suggest that AMPK functions are crucial for energy metabolism of colorectal cancer peritoneal carcinomatosis, and regulation of AMPK activity could be a potential molecular target for the treatment of CRC-pc.

Citation Format: Fabio Bozzi, Angela Mogavero, Luca Varinelli, Annunziata Gloghini, Valerio Leoni, Galina V. Beznoussenko, Alexandre A. Mironov, Ermanno Leo, Marco A. Pierotti, Italia Bongarzone, Manuela Gariboldi. Disruption of energy homeostasis as an approach to block the proliferation of colon carcinomatosis. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr B19.
Abstract B27: Serum uric acid levels as a prognostic factor in male patients with non-metastatic colorectal cancer
Authors: Rumi Shin , Won Park Ji , Woon Lee Dong , Seung-Bum Ryoo , Seung-Yong Jeong
Published: March 2017

Objective: Uric acid may be a marker of oxidative stress, and can be act as an antioxidant or a prooxidant. The role of serum uric acid (SUA) in the prognostic impact of cancer is controversial. This study aimed to evaluate whether the preoperative SUA level is associated with long-term outcomes in patients with colorectal cancer (CRC).

Methods: Between 2002 and 2010, 2,183 patients, who underwent curative surgical resection for non-metastatic CRC and had available SUA value, were included for this study. We analyzed the association between the overall survival (OS) and SUA level as quartile according to sex, using log-rank test and Cox proportional hazard regression to identify prognostic factors.

Results: Mean SUA level was different between male and female (male [n=1,328]: 5.320 ± 1.363, female [n=855]: 4.065 ± 1.180, p<0.001). In female patients, there was no difference in OS according to SUA level. In male patients, SUA levels in the lowest quartile (< 3.5 mg/dL) was associated with poor overall survival (5-year OS of SUA level < 3.5 mg/dL vs ≥ 3.5 mg/dL: 72.0 % vs 97.1 %, p < 0.001). SUA level was an independently significant prognostic factor (HR 1.714, 95% CI 1.306-2.250, p<0.001).

Conclusion: Our results do not support the protective role of SUA in CRC cancer, and rather lower SUA concentrations to be associated with poor long-term outcomes in male CRC patients.

Citation Format: Shin Rumi, Park Ji Won, Lee Dong Woon, Ryoo Seung-Bum, Jeong Seung-Yong. Serum uric acid levels as a prognostic factor in male patients with non-metastatic colorectal cancer. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr B27.
Abstract IA18: Noncoding RNA biomarkers in gastrointestinal cancers
Authors: Goel Ajay
Published: March 2017

Cancer has emerged as a leading cause of mortality worldwide, claiming over 8 million lives annually. Gastrointestinal (GI) cancers account for ~35% of these mortalities. Recent advances in diagnostic and treatment strategies have reduced mortality among GI cancer patients, yet a significant number of patients still develop late-stage cancer, where treatment options are inadequate. Emerging interests in “liquid biopsies” have encouraged investigators to identify and develop clinically-relevant noninvasive genomic and epigenomic signatures that can be exploited both as biomarkers capable of detecting premalignant and early-stage cancers, and as therapeutics for targeted cancer treatment. In this context, microRNAs (miRNAs), which are small non-coding RNAs that are frequently dysregulated in cancers have emerged as promising entities for development as liquid biopsy biomarkers. Albeit the future looks promising, current approaches for detecting miRNAs in blood and other biofluids remain inadequate. This presentation will summarize an update on exploiting circulating miRNAs as cancer biomarkers and evaluating their potential as tissue-based, and more importantly as liquid biopsies in GI cancers.

Citation Format: Ajay Goel. Noncoding RNA biomarkers in gastrointestinal cancers. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr IA18.
Abstract IA22: Clonal evolution and drug resistance in colorectal cancers: The EGFR-RAS signaling pathway
Authors: Bardelli Alberto
Published: March 2017

When metastatic colorectal cancers are challenged with targeted agents almost invariably a subset of cells insensitive to the drug emerges. As a result, in most instances, targeted therapies are only transiently effective in patients. Strategies to prevent or overcome resistance are therefore essential to design the next generation of clinical trials. How can we overcome the near-certainty of disease recurrence following treatment with targeted agents? To address this question a deeper understanding of the evolutive nature of cancer cells is necessary. We used colorectal cancer (CRC) as a model system to test the hypothesis that by understanding tumor's evolution the emergence of drug resistance can be controlled. We find that clonal dynamics can be monitored in real time in the blood of patients, and liquid biopsies can be used to intercept the emergence of resistant clones before relapses are clinically manifest. We discovered that a multistep clonal evolution process driven by progressive increases in drug fitness underlies the development of resistance in cells and patient avatars. To have long-term efficacy, the use of targeted therapies must take into account the continuous evolution of cancer cells, that is to say, therapies must adapt to tumor evolution. One possibility is to anticipate the changes the tumors will make. For example, by knowing in advance how CRC cells overcome resistance to EGFR blockade, we devised further rounds of therapy. Another approach is to unleash the ability of cancer cells to be recognized by the immune system. We tested this possibility in syngeneic mouse models of colorectal tumors. Our findings indicate that inactivation of DNA repair triggers dynamic neoantigen evolution; impairs cancer growth and leads to prolonged therapeutic responses.

Citation Format: Alberto Bardelli. Clonal evolution and drug resistance in colorectal cancers: The EGFR-RAS signaling pathway. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr IA22.
Abstract IA29: Eliminating racial disparities in colorectal cancer
Authors: Grubbs Stephen
Published: March 2017

The Delaware Cancer Advisory Council was convened in 2001 by Governor Ruth Ann Minner to develop a statewide cancer control program. Rather than reporting a comprehensive cancer control program, the Council in 2002 recommended a limited number of achievable deliverables to reduce Delaware's high rates of cancer incidence and mortality. The Delaware Legislature and the Governor Minner accepted the recommendations and fully funded the program. Three key elements of the program include a statewide coordinated colorectal screening program with coverage of the uninsured, a cancer treatment program providing for the uninsured, and an emphasis of African American cancer disparity reduction. The screening program featured statewide nurse navigation, colonoscopy promotion, statewide marketing, and coverage for both screening and up to two years of cancer treatment for the uninsured.

Over the next ten years, the program eliminated the Caucasian and African American colorectal cancer disparities between by raising screening rates, lowering the stage at diagnosis, reducing the incidence, and finally eliminating the mortality disparity. All Delaware populations achieved improved colorectal cancer outcomes with the greatest gain in the African American community that closed the disparity gaps.

Delaware can be viewed as a model for success, achieved when all parties including government, health care systems, providers, and the public are determined together to improve health and tackle health disparities.

Citation Format: Stephen Grubbs. Eliminating racial disparities in colorectal cancer. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr IA29.
Abstract PR03: The pig as a model for colorectal cancer
Authors: Wander Carolin , Flisikowska Tatiana , Flisikowski Krzysztof , Schulze Érica , Fries Hans-Rudolf , Bauersachs Stefan , Kind Alexander , Schnieke Angelika
Published: March 2017

Colorectal cancer is the fourth most common cancer worldwide with a mortality of more than 50%. Contrary to the increasing advances in cancer research colorectal cancer deaths are increasing in number. Most animal models also for colorectal cancer are in rodents. However, mice differ significantly in size, lifespan, physiology, anatomy and diet. Furthermore, genetically engineered mouse models for colorectal cancer show polyp development in the small intestine, contrary to the human phenotype that develops polyps in the large intestine. Therefore, a more suitable animal model is necessary. Pigs are increasingly recognized as a valuable model facilitating diagnostic and therapeutic strategies at human scale, longitudinal studies of disease initiation, progression and treatment response in preclinical trials.

We generated gene targeted cloned pigs carrying the nonsense mutation, APC1311 that is orthologous to a human mutation associated with a very severe phenotype of colorectal cancer and the inherited condition familial adenomatous polyposis (FAP). In pigs the APC1311 mutation results in multiple adenomatous polyps in the colon and rectum that, so far, have progressed to carcinoma in situ. Histological and molecular analysis show that the porcine model recapitulates all major features of early stage human FAP. Breeding and analysis of the mutant pig herd has revealed segregation of traits that affect polyposis severity in animals carrying the same APC1311 mutation. We are currently investigating the genetic basis for this effect by comparing normal mucosa samples from low and high polyp animals and have discovered some genes that are differentially expressed. A progression study comparing low-grade with high-grade adenomas also identified differentially expressed genes and miRNAs.

Further improvements of this model are targeted at generating organ/tissue specific Cre pigs to activate latent mutations such as KRAS and TP53 mutations in the colon. Additionally to encourage cancer progression we are working on the introduction of ubiquitous Cas9 expression in our APC1311 pigs to allow the activation of oncogenic pathways locally in vivo.

Our porcine model provides a powerful new resource for preclinical cancer research, including identifying and investigating novel biomarkers for early detection.

This abstract is also being presented as Poster A20.

Citation Format: Carolin Wander, Tatiana Flisikowska, Krzysztof Flisikowski, Érica Schulze, Hans-Rudolf Fries, Stefan Bauersachs, Alexander Kind, Angelika Schnieke. The pig as a model for colorectal cancer. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr PR03.
Abstract A10: Correlating magnetic resonance and molecular imaging using three dimensional untreated virtual control
Authors: Jacobs Joshua , Hawkins-Darrud Andrea , Harrison Robert , Johnston Sandra , Kinahan Paul , Swanson Kristin
Published: March 2017

With mean survival from glioblastoma multiforme (GBM) barely edging over 15 months, it become imperative to develop novel tools informing on both progression and treatment efficacy. As the aggressive growth of GBM outstrips available resources, regions of hypoxia develop. Hypoxia can be clinically assessed through [18F]-flouromisonidazole (FMISO) PET. However, PET imaging suffers from low resolution and reconstruction artifact. We present the comparative and predictive results of a multi-stage model utilizing the mathematical biology of cancer and the physics of PET imaging.

Our mathematical model of GBM characterizes cancer cells into the interacting phenotypes of normoxic, hypoxic, and necrotic cells supported by vasculature. The pharmacokinetic activity of FMISO is induced in the simulated tissue then acquired and reconstructed by an analytic simulator of the PET process. This multi-stage process creates a patient-specific virtual PET images with characteristic of the clinical PET scan. Extending previous work, we model the full three-dimensional dynamics of tumor progression, pharmacokinetic activity, and FMISO PET for the tumor kinetics of six GBM patients. Virtual and clinical FMISO PET images are compared.

Overall hypoxic burden and spatial distribution show strong correspondence between virtual and clinical FMISO PET images for all six patients.

Simulated FMISO PET dynamics, with tumor kinetics derived from routine clinical MRI scans, provide a unique and evolving tool giving insight into the biological connections between magnetic resonance and molecular imaging.

Citation Format: Joshua Jacobs, Andrea Hawkins-Darrud, Robert Harrison, Sandra Johnston, Paul Kinahan, Kristin Swanson. Correlating magnetic resonance and molecular imaging using three dimensional untreated virtual control. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr A10.
Abstract A20: Use of cell-free plasma DNA for dynamic monitoring of response to cytotoxic chemotherapy
Authors: Ruderman Daniel , Patsch Katherin , Matasci Naim , Soundararajan Anjana , Diaz Patricia , Gross Mitchell E.
Published: March 2017

Background: There is great interest in utilizing blood-based circulating biomarkers to gain molecular insight into cancer. Most of the published data examines circulating free DNA (cfDNA) obtained at a single time-point. Here, we developed and utilized an methodology for monitoring cfDNA at multiple time-points within 24 hours of cytotoxic chemotherapy infusions over sequential cycles.

Methods: To monitor the short- and long-term responses to treatment, we analyzed cfDNA from plasma drawn immediately before (baseline), 5 hours and 24 hours after administration of docetaxel chemotherapy. We quantified the extracted cfDNA via qPCR of Long interspersed nuclear elements (LINE1). We then amplified and performed targeted deep sequencing (Illumina Miseq) of androgen receptor (AR) exon 8. To reduce PCR variability, we pooled 10 technical replicate amplifications.

Results: Detailed data and time courses are presented for a patient with castrate resistant prostate cancer metastatic to bone treated with docetaxel/everolimus/bevacizumab according to a recently published trial (J Clin Oncol 33, 2015 suppl; abstr 5066). LINE1 was measured at 34.4 pg/mcl at baseline prior to treatment. Targeted deep sequencing of AR exon 8 revealed two independent mutations at 11% (H874A) and 13% (T877A), respectively. 5 hours after start of docetaxel infusion, total DNA content measured by LINE1 decreased to 0.4 pg/mcl. However, H874A and T877A mutations were observed at frequencies similar to the baseline values. A similar pattern was observed for samples obtained at Cycle 2 (21 days later). Specifically, baseline values for LINE1 (67.4 pg/mcl), H874A (3%), and T877A (7%) were noted to change to LINE1 (8.5 pg/mcl), H874A (6%), and T877A (17%) 5 hours later.

Conclusion: We conclude that cytotoxic chemotherapy can produce effects immediately observable on cfDNA markers. The generalizability and clinical relevance of these findings will require follow up studies involving more patients.

Citation Format: Daniel Ruderman, Katherin Patsch, Naim Matasci, Anjana Soundararajan, Patricia Diaz, Mitchell E. Gross. Use of cell-free plasma DNA for dynamic monitoring of response to cytotoxic chemotherapy. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr A20.
Abstract A24: ZAP-70 and SYK regulation in the B cell receptor pathway in chronic lymphocytic leukemia
Authors: Frushicheva Maria P.
Published: March 2017

Recent discoveries of inhibitors for Syk (spleen tyrosine kinase) family protein kinases provide promising therapeutic options for patients with chronic lymphocytic leukemia (CLL). However, molecular mechanisms of these inhibitors in the B cell receptor (BCR) signaling pathway are not well understood. This study investigates functionality of Syk family protein kinases and their inhibitors in the BCR signaling pathway in CLL cells. In this work, we tested several computational models of ZAP-70 (ζ chain–associated protein kinase of 70 kD) and SYK regulation in the BCR signaling pathway to explain the observed differences in the clinical behaviors of ZAP-70+ / ZAP-70- phenotypes of CLL patients. Specifically, we characterized the effects of different ZAP-70 and SYK expression and phosphorylation levels on the BCR activation threshold. Using stochastic simulations of BCR signaling network, we reproduced the correlations between the observed and calculated trends quantitatively. We find that an increased ZAP-70 expression is correlated with decreased levels of phosphorylated ZAP-70 and SYK, depending on the amount of SYK that is expressed in cells. Our calculations also show that ZAP-70 is able to compensate for a missing SYK functionality with an increased BCR activation threshold in SYK-deficient B-CLL cells, similar to SYK-deficient B cells. Furthermore, our computational model predicts a dual inhibition of ZAP-70 and SYK for the treatment of ZAP-70+ patients, as a selective inhibition of either ZAP-70 or SYK results in disease relapse. Our findings uncover molecular mechanisms of ZAP-70 and SYK regulation in the BCR signaling pathway for the development of CLL immunotherapies.

Citation Format: Maria P. Frushicheva. ZAP-70 and SYK regulation in the B cell receptor pathway in chronic lymphocytic leukemia. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr A24.
Abstract A25: Systems biology approach to delineating DNA damage response and R-loop dependencies in Ewing sarcoma
Authors: Gorthi Aparna , Loranc Eva , Lin Cao , Bishop Alexander JR
Published: March 2017

Ewing sarcoma is a rare, yet highly aggressive family of bone and soft tissue tumors that afflicts children and young adults. It is the prototypical example of mesenchymal tumors driven by a fusion oncogene involving the EWSR1 gene, most frequently EWS-FLI1. Ewing sarcoma is exquisitely sensitive to genotoxic agents, and more recently PARP1 inhibitors, predominantly when detected at an early stage. However, the molecular basis for this sensitivity is relatively under-explored. Further, the long term side effects of these drugs pose a critical barrier to effective treatment. In this study, we proposed to delineate the pathways dictating Ewing sarcoma chemosensitivity and identify alternative avenues for targeted therapy.

R-loops are three nucleic acid DNA structures consisting of an RNA:DNA hybrid and a displaced complementary DNA loop. The importance of R-loops in both being causative as well as disruptive in DNA damage as well as DNA damage response has emerged through recent studies. Our previous work has demonstrated that Ewing sarcoma cell lines have high levels of endogenous damage as well as replication stress. We observe that Ewing cell lines have elevated levels of persistent R-loops and impaired homologous recombination repair of double strand breaks. In the present study, we use a multimodal, systems biology approach involving high-throughput RNAi based survival data, time-course RNA-seq in response to two chemotherapeutics, Chromatin immunoprecipitation-seq and DNA:RNA hybrid immunoprecipitation-seq datasets across multiple Ewing sarcoma and control cell lines. Our data led to the identification of a subset of genes whose expression patterns in response to DNA damage is dysregulated in Ewing sarcoma. Predominantly, among these genes is a network of RNA binding proteins that highlights the importance of RNA metabolism in DNA damage response. We also observe a concomitant alteration in damage-dependent transcription. Finally, we identified several compensatory mechanisms that are upregulated in Ewing sarcoma (RNASEH2, FEN1, Fanconi Anemia, etc.) in order to manage the exacerbated genomic stress conditions and targeting any of these pathways leads to severe tumor cell cytotoxicity. We therefore propose the use of these pathways as potential candidates for targeted therapy.

Citation Format: Aparna Gorthi, Eva Loranc, Cao Lin, Alexander JR Bishop. Systems biology approach to delineating DNA damage response and R-loop dependencies in Ewing sarcoma. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr A25.
Abstract A32: Tumor-matrix tnteractions in early ductal invasions: Integrating histology imaging with computational modeling
Authors: Rejniak Katarzyna A. , Lloyd Mark C. , Kasprzak Agnieszka , Bui Marilyn
Published: March 2017

Progression from a ductal carcinoma in situ (DCIS) to an invasive tumor is a major step initiating a devastating and often lethal metastatic cascade. One sentinel event that initiate this process is the development of ductal microinvasions, i.e., small cohorts of tumor cells that breach the basement membrane surrounding the duct, and migrate through the extracellular matrix (ECM). This process is difficult to reproduce experimentally and investigate in a fully controlled way. However, mathematical modeling based on physical principles and medical imaging can shed light on interactions between tumor cells and the surrounding stroma during the spread of microinvasions.

We used a combination of advanced image analysis techniques applied to patients' histology data, that include both tissue regions and single cells segmentation, with multi-factorial classification to extract feature data which identifies specific properties of individual tumor cells inside the duct and on the invasive front. These histology-based quantitative data were then used to calibrate a hybrid agent-based mathematical model of DCIS-ECM interactions that takes into account both individual tumor cells and the underlying ECM fibril structure. The model was employed in a computational simulation study to delineate physical properties of the matrix fibers that can facilitate and/or prevent formation and progression of ductal microinvasions.

Our integrated approach incorporating medical imaging and computational modeling, allowed us to predict the dynamics of emerging ductal microinvasions that are consistent with the observed clinical data. We showed how changes in the local microenvironmental niche near the DCIS edge leads to initiation of ductal microinvasions. We identified physical properties of the matrix that can facilitate or prevent the progression of such microinvasions. Our methods also provide a tool for quantifying morphological and immunohistochemical properties of individual cells within the mammary ducts and ductal microinvasion, as well as a tool for testing biomechanical hypotheses of tumor cell-tumor matrix interactions.

These findings can be directly compared to the patient histology samples and can lead to development of new prognostic methods and therapeutic interventions by targeting the tumor preinvasive niche.

Citation Format: Katarzyna A. Rejniak, Mark C. Lloyd, Agnieszka Kasprzak, Marilyn Bui. Tumor-matrix tnteractions in early ductal invasions: Integrating histology imaging with computational modeling. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr A32.
Abstract A37: ‘Touch-and-go' behavior of cancer cells in spatially-confined, fiber-like microenvironments
Authors: Milano Daniel , Muthuswamy Senthil , Asthagiri Anand
Published: March 2017

In a crowded, fibrillar tumor microenvironment (TMEN), invading cancer cells encounter and interact with many other cells and cell types. Whether cancer cells stop migrating or reverse direction at every encounter with another cell, or circumnavigate and slide around the encounter, will affect the efficiency of the invasion process. We find that breast cancer cells migrating along fiber-like micropatterns (FLMs) respond differently to cell-cell encounters than what is expected based on the classically-established phenotype of contact-inhibition of locomotion (CIL). Cancer cells are remarkable efficient at sliding around other cancer cells, even along FLMs much narrower than their own cell body. In contrast, non-transformed breast epithelial cells reverse direction upon encountering other normal cells. Differences in cell size fail to predict these outcomes. Interestingly, the participation of normal cells in invasive sliding behavior increases when interacting with a cancer cell rather than another a normal cell. This induction of cancer-like behavior in normal cells suggests that heterotypic interactions between disparate cell types in the TMEN may produce synergistic, disease-promoting collective behaviors. Furthermore, using a series of individual and combinatorial genetic perturbations, we show that genetic factors (ErbB2, E-cadherin, PARD3, TGFbeta) quantitatively shift the ability of normal cells to slide. Specifically, successive genetic perturbations enable normal cells to slide on progressively narrower FLMs. These results suggest that as fibers align and mature during cancer progression, coincident genetic perturbations enable cells to take advantage of the widening fibrillar tracks to execute slides and achieve more efficient dispersion in a crowded microenvironment.

Citation Format: Daniel Milano, Senthil Muthuswamy, Anand Asthagiri. ‘Touch-and-go' behavior of cancer cells in spatially-confined, fiber-like microenvironments. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr A37.
Abstract A41: Biomechanics: A new therapeutic innovation deposit – From the proof of concept to the proof of efficacy
Authors: Brossel Remy
Published: March 2017

Malignant tissue can be normalized in vitro using mechanical signals. A biomechanical treatment has been applied to a tumor of human origin grafted subcutaneously in mice and demonstrated the normalizing effect of stress on tumor growth in vivo. Following this Proof of Concept, a feasibility study has been performed to build a prototype for a Proof of Efficacy: Application of a Constraint Field on human pancreatic cancer grafted in the pancreas of mice. Two devices are combined to generate the local constraint: First a generator of Gradient of Magnetic Field (GMF), second magnetizable iron nanoparticles located in the neovessels surrounding the tumor itself. Nanoparticles act as bioactuators transforming magnetic energy in mechanical energy. This feasibility study was performed on the GMF generator with two opposite permanent magnets. The pressure (Pa) created on the neovessels is: P = Fv.L.Ms,v.dB/dx

L is the stroma thickness (m);

Fv is the nanoparticle volume proportion of stroma;

Ms,v is the magnetization of nanoparticles (A/m);

dB/dx is the magnetic induction gradient in stroma thickness direction (T/m).

Iron-core coils are the best means to obtain our goal: A magnetic pressure of about 100 to 500 Pa on the tumor surface. The tumor is a one-centimeter-diameter sphere located at the center of our measured zone, a tube with 3 cm square section.

Three dimensional magnetic simulations with a finite element method show that a magnetic induction gradient of 50 T/m is achievable. This gradient can be maintained permanently, can vary with time, and can have a variable direction in the field of study.

The other variables that increase pressure are: The proportion of iron particles (greater than 100 mg/ml), the thickness of stroma, and the magnetization of particles.

The experimental laboratory environment in which the anesthetized rodents are studied must permit heat dissipation to obtain reproducible results with no influence of temperature. The power losses do not exceed 600 watts, so the use of air-cooling is adequate.

The magnetic induction gradients are strong, but obtainable at the tumor-stroma interface. The progression to a whole human prototype will necessarily require supra-conductor coils.

We will present the data on changes in in vivo human tumor size and configuration with the application of external quantifiable constraint field in the experimental mouse.

Citation Format: Remy Brossel. Biomechanics: A new therapeutic innovation deposit – From the proof of concept to the proof of efficacy. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr A41.
Abstract A49: Tumor-associated interstitial flow promotes macrophage migration and pro-metastatic M2 phenotype in 3D ECM
Authors: Li Ran , Xing Hao , Lee Tara A. , Azizgolshani Hesham , Kamm Roger D.
Published: March 2017

The growth of solid tumor is often accompanied by an increase in the flow of interstitial fluid (interstitial flow) from the center of the tumor to the surrounding stroma. Recent studies have shown that elevated interstitial flow can influence the migration of cancer cells and fibroblasts. Despite these findings, the effects of interstitial flow on macrophages, one of the key metastasis-promoting tumor-associated stromal cell types, have not been explored. We used microfluidic and transwell flow assays to investigate how high level of interstitial flow (~3 μm/s) often observed in tumor affect macrophage migration and protein expression. We found that interstitial flow not only enhanced macrophage migration speed, but also directed macrophages to migrate against the flow in 3D extracellular matrix. Moreover, we discovered that interstitial flow activated Akt and FAK, two kinases that are crucial for cell migration. Interestingly, interstitial flow also up-regulated macrophage expression of M2 markers Arg I and TGFβ through the activation of JAK1-STAT3/6 pathway. Finally, macrophages treated with interstitial flow were shown to have enhanced abilities to promote cancer cell migration and protrusion formation. Taken together, these results suggest that interstitial flow can promote metastasis through its effects on macrophages. Specifically, since macrophages migrate against the flow, interstitial flow, which emanates from the tumor, can act as a mechanical stimulus to recruit macrophages into tumor tissues. Moreover, interstitial flow can activate macrophages and polarize them toward pro-metastatic M2 phenotype to further promote tumor metastasis and immunosuppression.

Citation Format: Ran Li, Hao Xing, Tara A. Lee, Hesham Azizgolshani, Roger D. Kamm. Tumor-associated interstitial flow promotes macrophage migration and pro-metastatic M2 phenotype in 3D ECM. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr A49.
Abstract A63: Collective and individual migration after the epithelial-mesenchymal transition in engineered microenvironments
Authors: Wong Ian Y.
Published: March 2017

Scattering and local dissemination of individual cells from a collective invasion front has been associated with the epithelial-mesenchymal transition (EMT). This phenotypic heterogeneity and plasticity has been challenging to reconstruct using classical assays which only measure population averages at endpoints. Here, we comprehensively track single cell invasion dynamics within engineered microenvironments such as microfabricated pillar arrays as well as 3D biomaterial scaffolds. After EMT induction through the master regulator Snail in mammary epithelial cells, we find distinct phenotypic subpopulations that display collective or individual migration behaviors. We show that these complex behaviors can be physically understood in terms of a phase transition during the solidification of binary alloys. Biologically, this conceptual framework addresses two essential mechanisms—phenotypic cell sorting and interconversion. We present new results to corroborate this model by systematically varying the composition of mosaic populations with both epithelial and EMT phenotypes. We also perturb these behaviors using migration-inhibiting compounds, revealing that different invasion phenotypes are correlated with differences in drug sensitivity. Altogether, this integration of engineered microenvironments with single cell resolution may permit new quantitative insights into the interplay of invasion, drug resistance and heterogeneity.

Citation Format: Ian Y. Wong. Collective and individual migration after the epithelial-mesenchymal transition in engineered microenvironments. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr A63.
Abstract B04: From modeling to in vivo tracking: a new platform for the design of delivery vectors that exploit tumor microfluidics
Authors: Nizzero Sara , Litvinov Sergey , Alexeev Dmitry , Economides Athena , Rosa Enrica De , Wolfram Joy , Koumoutsakos Petros , Ferrari Mauro
Published: March 2017

Within the field of oncology, a new perspective has recently emerged, where cancer treatment is viewed as a transport problem that can be addressed with nanomedicine. In fact, because of the unique local conditions of transport and microfluidics in the tumor environment, microparticles and nanoparticles that exhibit specific geometries have proven advantageous to enhance preferential delivery of drugs to tumor tissue. However, the theoretical and modeling backbone required to describe, understand, and manipulate such flow-specific design advantages is currently limited to semi-analytical methods. These methods have proven successful in explaining the power and efficacy of geometrical targeting. Nevertheless, since such approaches have limited predictive power, they are not ideal tools for the systematic development of a new class of efficient and customizable delivery vectors.

In this work, we propose an innovative and rational approach for understanding the delivery of micro- and nanotherapeutics to cancer tissue by modeling transport in tumor microvessels. Specifically, we focus on the differences between healthy and tumor vasculature that affect fluid mechanics.

We tackle this problem with a combined experimental and modeling approach. Our model is based on a Navier-Stokes solver for complex fluids based on dissipative particle dynamics (DPD) simulations, where blood constituents (i.e. red blood cells, neutrophils, platelets) and microparticles/nanoparticles interact through forces or collisions of different nature. The model is calibrated and validated with real-time flow chamber experiments. With this modeling approach, complex geometrical structures and interactions can be implemented with high computational efficiency. We use our innovative platform to analyze the differences in margination of micro- and nanostructures in tumor versus healthy microvasculature. We address the fundamental structural differences between tumor vessels and healthy vessels by systematically reconstructing the characteristic patterns of endothelial fenestrations, radius variability, and blood flow. Our parametric analysis is then compared with in vivo tracking studies in animal models.

Our approach and results open the way to the understanding and rational design of a new class of nanoparticle and microparticle-based delivery strategies that exploit tumor-specific microfluidics.

Citation Format: Sara Nizzero, Sergey Litvinov, Dmitry Alexeev, Athena Economides, Enrica De Rosa, Joy Wolfram, Petros Koumoutsakos, Mauro Ferrari. From modeling to in vivo tracking: a new platform for the design of delivery vectors that exploit tumor microfluidics. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr B04.