bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2068: Single-cell RNA-seq profiling of the transcriptional response to Rb loss in the retinoblastoma cell of origin
Authors: Lee Sunhye , Singh Hardeep P. , Triska Martin , Stachelek Kevin T. , Bay Maxwell M. , Grubbs Brendan H. , Thronton Matthew E. , Hu Haoze , Segil Neil I. , Bonaguidi Michael A. , Cobrinik David
Published: August 2018

Retinoblastoma is a rare childhood tumor initiated by biallelic inactivation of the RB1 gene and loss of functional retinoblastoma (Rb) protein. The tumors are thought to originate in cone photoreceptor precursors since Rb knockdown induces cone precursor proliferation and elicits cone-precursor-derived retinoblastoma-like tumors in orthotopic grafts. The identification of the retinoblastoma cell of origin and the authentic initiating mutation presents an opportunity to define the detailed molecular mechanisms controlling malignant transformation of a human cancer. In this project, we seek to define the transcriptional and epigenetic cell state transitions that follow Rb depletion as post-mitotic human cone precursors are induced to re-enter the cell cycle. Prospectively isolated cone precursors were transduced with lentivirus carrying either of three RB1 shRNAs or a SCR control shRNA and then re-isolated by FACS. Single cell RNA-sequencing (scRNA-seq) was performed at multiple time points over 15 days by generating full-length cDNAs corresponding to polyadenylated RNAs followed by sequencing. Among the 572 individual cells that passed quality control, an average of 6.6 million mapped reads and ~21,000 genes (~93,000 transcript isoforms) were detected per transcriptome. In addition, 300 cells per shRNA group were evaluated for genome-wide open chromatin using uATAC-seq at day 0 and 15. Cell transcriptomes were pseudotemporally ordered using “Waterfall” in order to define cellular trajectories and corresponding transcriptomic responses to Rb loss. Using transcriptomic, epigenetic, and network analyses, we define cell state transitions and identify potential mediators of such transitions, that are associated with the initiation of retinoblastoma development.

Citation Format: Sunhye Lee, Hardeep P. Singh, Martin Triska, Kevin T. Stachelek, Maxwell M. Bay, Brendan H. Grubbs, Matthew E. Thronton, Haoze Hu, Neil I. Segil, Michael A. Bonaguidi, David Cobrinik. Single-cell RNA-seq profiling of the transcriptional response to Rb loss in the retinoblastoma cell of origin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2068.
Abstract 2083: Innate immunity polymorphisms and risk of pediatric cancer
Authors: Mercado Gabriela E. , Rosales-Bravo Gabriela A. , Velazquez-Fernandez David , Zapata-Tarres Marta , Juarez-Villegas Luis E.
Published: August 2018

In Mexico, cancer represents the second leading cause of death in the pediatric population. The identification of susceptibility genes associated with cancer has been one of the main challenges of human genomics. Several studies have proposed that genetic variation in immune-related genes could be a determinant of susceptibility in different types of cancer. In the present study we evaluated the possible association between 10 polymorphisms in genes that participate in innate immunity and the risk of pediatric cancer. We analyzed genotyping data from 101 patients from Hospital Infantil de México “Federico Gómez” (HIM) with confirmed diagnosis of pediatric cancer. The genotypes were compared with 274 healthy adults without a medical history of pediatric cancer. For each polymorphism we calculated allelic and genotypic frequencies and Hardy-Weinberg equilibrium (HWE). The association between cancer and pediatric cancer was analyzed using Pearson chi-square and odds ratio (OR); survival analyses were performed by the log rank test and Kaplan-Meier curves. Our results show that risk of pediatric cancer in our sample is significantly associated with the genetic variants IL8-251 (p= 0.04327, OR= 0.701, IC 95% = 0.496-0.990), IL6-174 (p= 0.0037, OR= 2.413, IC 95% = 1.310-4.445), and IL10-592 (p= 0.0062, OR= 0.670, IC 95% = 0.502-0.894). However, we did not find any significant association between selected polymorphisms and overall or disease-free survival.

Citation Format: Gabriela E. Mercado, Gabriela A. Rosales-Bravo, David Velazquez-Fernandez, Marta Zapata-Tarres, Luis E. Juarez-Villegas. Innate immunity polymorphisms and risk of pediatric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2083.
Abstract 2109: Prognostic and functional significance of interleukin 22 in colorectal cancer
Authors: Cremonesi Eleonora , Tosti Nadia , Amicarella Francesca , Weixler Benjamin , Däster Silvio , Governa Valeria , Spagnoli Giulio C. , Terracciano Luigi , Tornillo Luigi , Eppenberger-Castori Serenella , Iezzi Giandomenica , Droeser Raoul
Published: August 2018

T cell infiltration has been recognized to significantly impact clinical outcome in human colorectal cancer (CRC). Interleukin 22 (IL-22), a cytokine secreted by IL-17-producing CD4+ T cells (Th17) is known to play a crucial role in inflammatory bowel disease and has been shown to have protumorigenic activity in mouse tumor models. However, its role in human CRC is still unclear. In a previous study we could demonstrate the dual role of Th17 in CRC. As consequence we evaluated the prognostic and functional impact of IL-22 producing cells in human CRC in this follow-up study. Upon staining of a tissue microarray (TMA), including 423 CRC cases, IL-22 positive cells were detected both within tumor cells and tumor infiltrating immune cells. Whereas, IL-22 expression by tumor cells did not impact on prognosis, densities of IL-22 positive immune cells were found to be significantly associated with early T stage and MMR-deficient microsatellite stability. Importantly, IL-22 expression by CRC infiltrating immune cells was predictive of improved overall survival independent of known prognostic factors such as T stage, N stage, tumor grade, vascular invasion, tumor border configuration and MMR status. Phenotypic characterization of IL-22 positive cells performed by flow cytometry revealed that they consist mainly of Th17 cells, also producing IL-17. In vitro experiments showed no direct effect of IL-22 on CRC cell proliferation. On-going studies are validating the prognostic effect on a TMA cohort with corresponding transcriptomic data and evaluating potential effects mediated by IL-22 on other cell types of CRC microenvironment.

Citation Format: Eleonora Cremonesi, Nadia Tosti, Francesca Amicarella, Benjamin Weixler, Silvio Däster, Valeria Governa, Giulio C. Spagnoli, Luigi Terracciano, Luigi Tornillo, Serenella Eppenberger-Castori, Giandomenica Iezzi, Raoul Droeser. Prognostic and functional significance of interleukin 22 in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2109.
Abstract 2129: Breast tumor microenvironment & metastasis is controlled by activity of a2 isoform of V-ATPase in mammary epithelium
Authors: Katara Gajendra K. , Kulshrestha Arpita , Sahoo Manoranjan , Beaman Kenneth
Published: August 2018

Extracellular matrix (ECM) critically impacts tumor progression and is influenced by both cancer and host tissue cells. While our understanding of cancer cell ECM remodeling is widespread, the importance of host tissue ECM, which provides an initial congenial environment for primary tumor formation, is only partly understood. Previously, we have shown that epithelial cell associated vacuolar (V)-ATPase ‘a2' isoform (a2V) regulates stiffness of mammary gland ECM. Here, we investigated how a2V mediated alterations in ECM of breast tissues affects the tumor microenvironment and metastasis of breast cancer. We also established the correlation of a2V expression in the normal breast tissue with metastatic occurrence in cancer patients. In this study, using the MMTV-Cre-Lox system, we deleted the a2V gene in epithelial cells of mouse mammary glands. Tumors were transplanted in mammary fat pads of a2V conditional knockout mice (a2VcKO) using E0771/Py230 mouse mammary cancer cells. These tumors were evaluated for the histopathology, ECM stiffness, immune cell populations, cytokines, angiogenic factors and metastasis. We show that in a2VcKO, breast tumors exhibit less tumor rigidity, increased inflammation and a more necrotic tumor microenvironment. These mice showed an increased metastasis of tumors compared to control evident by cytokeratin (Ck)14 staining of cancer cells in lung tissues (3.3 fold increase, P=0.004). Immuno-phenotyping of breast tumor microenvironment revealed increased infiltration of CD45 cells with higher number of anti-tumor M1 macrophages (2.1 fold increase, P=0.007) and elevated expression of inflammatory cytokines TNF-α and iNOS in a2VcKO mice compared to control (P=0.01). The tumors in a2VcKO mice were much more highly vascularized and angiogenic compared to control (P=0.01) evident by increased number of Meca32+SMA+ cells. Clinically, in cancer patients, low a2V expression levels in normal breast tissue correlated directly with lymph-node metastasis. Thus, this study has identified a2V expression in epithelial cells as a key modulator of tumor microenvironment and its expression levels can significantly modulate breast tumor dissemination.

Citation Format: Gajendra K. Katara, Arpita Kulshrestha, Manoranjan Sahoo, Kenneth Beaman. Breast tumor microenvironment & metastasis is controlled by activity of a2 isoform of V-ATPase in mammary epithelium [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2129.
Abstract 2154: A potent and orally available tubulin inhibitor ABI-231 suppresses triple negative breast cancer tumor growth and metastasis
Authors: Deng Shanshan , Krutilina Raya , Wang Qinghui , Seagroves Tiffany N. , Miller Duane D. , Li Wei
Published: August 2018

Triple-negative breast cancer (TNBC) is the most aggressive type and accounts for at least 15% of all types of breast cancer in the USA. TNBC is defined as tumors that lack the expression of estrogen receptor, progesterone receptor and human epithermal growth factor 2, and it is always characterized by poor prognosis due to the lack of molecular targets and the rapid development of resistance to many chemotherapeutic drugs. Interfering with microtubule dynamics is a validated drug target. Currently, one of the standard cares for TNBC treatment is using taxanes based chemotherapy, such as paclitaxel, which targets microtubules. However, drug resistance and neurotoxicities often limit their clinical efficacy, thus there are continuous needs to develop more effective therapies that could overcome these clinical limitations. In this study, we evaluated the preclinical efficacy of our potent tubulin inhibitor, ABI-231, in treating TNBC in mouse xenograft models. ABI-231 inhibited tubulin polymerization and effectively overcame P-gp mediated multidrug resistance, and it is orally available. ABI-231 showed remarkable anticancer activities against two TNBC cell lines at low nanomolar concentrations, and it could inhibit the cancer cell colony formation. Treatment with ABI-231 suppressed invasion and migration of TNBC cells, and significantly induced apoptosis of TNBC cells in vitro. ABI-231 inhibited TNBC tumor growth in a dose-dependent manner without acute toxicity in an orthotopic TNBC xenograft model. ABI-231 had similar efficacy to that of paclitaxel as tested in this mouse model. In addition, ABI-231 significantly reduced metastasis of TNBC in a tail vein mouse model. Collectively, these preliminary studies strongly suggest that ABI-231 is potent to inhibit the growth and metastasis of TNBC both in vitro and in vivo, and this potent tubulin inhibitor is a promising drug candidate for the more effective treatment of TNBC. Supported by NIH grant R01CA148706.

Citation Format: Shanshan Deng, Raya Krutilina, Qinghui Wang, Tiffany N. Seagroves, Duane D. Miller, Wei Li. A potent and orally available tubulin inhibitor ABI-231 suppresses triple negative breast cancer tumor growth and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2154.
Abstract 2156: Lung niche factors for progenitor cell self-renewal sustain lung cancer stem cells and contribute to drug resistance to kinase inhibitors in non-small cell lung cancer
Authors: Mitsui Akinori , Yokokawa Sachiko , Nagano Osamu , Saya Hideyuki
Published: August 2018

A mechanism underlying anti-cancer drug resistance relies on the existence of cancer stem cells (CSCs). However, CSCs are either absent or are few in number in xenograft tumors and syngeneic mouse models. We developed new lung cancer mouse models with CSCs to elucidate the role of CSCs in resistance to targeted therapeutics in non-small cell lung cancer (NSCLC). Mouse lung organoids containing progenitor cells were cultured in complete medium containing lung niche factors, FGF-10 and HGF, and were infected with a retrovirus encoding a Kras mutation (G12D), an Egfr deletion, and the EML4-ALK fusion protein. These induced CSCs were transplanted into mice, and the established tumors were cultured in vitro to test for drug sensitivity to trametinib, erlotinib, and crizotinib in the presence or absence of niche factors. The tumors that were poorly differentiated contained EpCAM-, Cd49f-, and Sca-1-positive CSCs. These mouse models allowed the prediction of clinical responses to targeted therapeutics, i.e., the tumor cells with the Egfr deletion and those with EML4-ALK fusion proteins showed strong responses to erlotinib and crizotinib, respectively. In addition, we found that Kras mutant cancer cells were resistant to trametinib due to activation of the HGF/Met pathway since HGF is an essential niche factor for lung progenitor cell proliferation. Combination treatment with trametinib and a Met inhibitor showed a synergistic effect in Kras mutant tumors. Based on these results, we propose a treatment approach that focuses on the use of niche factors for lung progenitor cells in NSCLC.

Citation Format: Akinori Mitsui, Sachiko Yokokawa, Osamu Nagano, Hideyuki Saya. Lung niche factors for progenitor cell self-renewal sustain lung cancer stem cells and contribute to drug resistance to kinase inhibitors in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2156.
Abstract 2157: Chemotherapeutic tolerability and estrogen dose response in the B6;129-Rag2
tm1Fwa
IL2rg
tm1Rsky/DwlHsd (R2G2) mouse model
Authors: Naden Jamie L. , Melton Michele , Bast Athena , Gardner Jermaine
Published: August 2018

The B6;129-Rag2tm1FwaIL2rgtm1Rsky/DwlHsd (R2G2) knockout mouse was developed by backcrossing an IL2rg (common gamma) knockout model to a RAG2 (recombinase activating gene) knockout model. The resulting mouse lacks various cytokines including IL-2, IL-4, IL-7, IL-9 and IL-15. In addition, this model lacks B cells, T cells, NK cells and has a deficit in lymphocyte development. This model was developed to provide another immunodeficient option for the oncology and immunology fields. The literature supports better tolerability of DNA-damaging oncology treatments for models that do not carry the SCID mutation. We have already reported in a white paper that the R2G2 mouse model is more tolerant of whole-body radiation than a model with the SCID mutation. Herein we describe a study examining chemotherapeutic tolerability of common DNA-damaging oncology drugs including 5-fluorouracil (5-FU), doxorubicin (Doxo), and cyclophosphamide (CTX) (n = 10 per group). 5-FU was given at 30, 60 or 100 mg/kg, intraperitoneally, twice weekly for five weeks. Doxo was given at 2 or 5 mg/kg, intraperitoneally, once weekly for three weeks. CTX was given at 100 or 140 mg/kg intraperitoneally, once weekly for three weeks. The low dose was chosen based on the average dose used in immunodeficient mouse models and the high dose was chosen based on the average dose used in immunocompetent mouse models. This was done to determine if the R2G2 mouse model can tolerate higher doses of these chemotherapeutic agents compared to other immunodeficient mouse models. Results show that the R2G2 mouse model tolerates higher doses of these chemotherapeutic drugs than doses found in the literature for SCID models. Exogenous estrogen tolerance is another common concern in oncology research as some immunodeficient mouse models cannot tolerate the subcutaneous estrogen pellets, developing negative secondary effects resulting in removal from study. We performed an estrogen pellet dose-response study using four doses of 60-day release 17-β estradiol pellets at 0.18, 0.36, 0.72, and 1.7 mg/pellet (n = 10 per group). R2G2 mice show dose-dependent effects of estrogen on morbidity. These data will allow researchers to determine the optimal dose for use in the R2G2 model. In conclusion, these data support that the R2G2 mouse model may be a good alternative to SCID models when administering DNA-damaging chemotherapies or when estrogen supplementation is required for xenograft growth.

Citation Format: Jamie L. Naden, Michele Melton, Athena Bast, Jermaine Gardner. Chemotherapeutic tolerability and estrogen dose response in the B6;129-Rag2tm1FwaIL2rgtm1Rsky/DwlHsd (R2G2) mouse model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2157.
Abstract 2160: MEN1611, a novel α-selective PI3K inhibitor in solid tumors
Authors: Merlino Giuseppe , Fiascarelli Alessio , Bigioni Mario , Bressan Alessandro , Irrissuto Clelia , Pellacani Andrea , Scaltriti Maurizio , Binaschi Monica
Published: August 2018

The PI3K pathway regulates various cellular processes such as proliferation, growth, apoptosis and cytoskeletal rearrangement. This pathway is frequently de-regulated and considered an oncogenic driver in human cancer. In most solid tumors, the activation of the PI3K pathway is induced by mutations of the catalytic subunit PI3Kα, present in approximately 20% to 50% of breast cancer, 14% of colorectal cancer and in 5-10% of NSCLC. Besides being an actionable target, the PI3K pathway is implicated in de novo and acquired treatment resistant in various tumor types treated with targeted therapy. As a matter of fact, the most interesting antitumor activity with PI3K inhibitors has been observed in combination. Here, we present MEN1611 (previously PA799), a PI3-kinase inhibitor with a peculiar biochemical profile targeting with high inhibition potency the mutated forms of PI3Kα and PI3Kγ. In the current study we demonstrate the anticancer activity and the pharmacodynamic effects of MEN1611 as monotherapy or in combination with targeted therapies in both xenograft and PDX models of breast cancer and in colorectal cancer and in NSCLC models, all with defined genetic profiles. MEN1611, at a clinically relevant dose, showed good antitumor activity in combination with targeted therapy agents against breast cancer, colorectal cancer and NSCLC models bearing PI3Kα mutations. A reduced activity was instead observed when the tumor models were wild type for PI3Kα or had low levels of PTEN. The antitumor activity of MEN611 was supported by its pharmacodynamic activity. In all the models, both AKT and S6 phosphorylation, markers of PI3K inhibition, were significantly inhibited upon treatment. In agreement with the biochemical profile of the drug, in PTEN null xenograft models where the tumor driver is the PI3K β-isoform, we observed lower effects in term of antitumor activity and of molecular inhibition of the pathway. Last, MEN1611 induction of hyperglycemia and insulin release was studied in the tumor models at clinical relevant dose as a marker of class-effect toxicity. MEN1611 showed significant antitumor activity in combination with other targeted therapies in breast, colon and NSCL cancer PI3Kα mutant models. Our results support the evidence that MEN611 is a PI3Kα specific inhibitor and provided the basis for the planned phase IB/II.

Citation Format: Giuseppe Merlino, Alessio Fiascarelli, Mario Bigioni, Alessandro Bressan, Clelia Irrissuto, Andrea Pellacani, Maurizio Scaltriti, Monica Binaschi. MEN1611, a novel α-selective PI3K inhibitor in solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2160.
Abstract 2185: Multiple region whole-genome sequencing reveals intratumor heterogeneity and branching clonal architecture of non-clear-cell renal cell carcinoma
Authors: Zhu* Bin , Poeta* Luana , Costantini* Manuela , Zhang* Tongwu , Sentinelli Steno , Shi Jianxin , Brown Kevin , Hua Xing , Yeager Meredith , Wang Mingyi , Hicks Belynda , Chanock* Stephen , Gallucci* Michele , Fazio* Vito , Landi* Maria Teresa
Published: August 2018

Limited knowledge about the intratumor heterogeneity (ITH) of non-clear-cell renal cell carcinoma (nccRCC) hinders therapeutic efficacy. We performed multi-region whole-genome sequencing, genome-wide methylation profiling and deep targeted sequencing of both primary and paired metastatic tumors in 124 samples from 29 subjects with papillary renal cell carcinoma type 1, papillary renal cell carcinoma type 2 and collecting duct kidney tumors. Samples were taken from the tumors' center to the periphery at ~1.5cm from each other. We conducted integrative ITH analysis of single nucleotide variants, somatic copy number alterations, structural variants, transposon element insertions, telomere length and DNA methylation, and inferred their respective evolutionary history. We also analyzed the concordance between physical and lineage phylogenetic evolution, and inferred the regions from which the metastases likely originated.

ITH varied significantly across tumors and histological subtypes. For example, the average number of structural variants per tumor was 1.2 in papillary RCC type 1 vs. 23.6 in papillary RCC type 2. In papillary tumors, ITH was lowest for copy number alterations (~5% subclonal changes across all tumor types), intermediate for single nucleotide variants (~32%), and highest for structural variants (~60%), suggesting a tumor molecular evolution along these steps. Lineage trees commonly showed branching evolutions with a dominant subclone. Focal deletion of the CDKN2A gene characterized the collecting duct tumors. Methylation ITH was highest in the enhancer regions. Metastatic and primary tumors shared similar mutation signatures. Telomere length was generally longer in normal vs. tumor samples and was similar in physically adjacent samples.

In summary, our study characterized ITH of nccRCC with unprecedented details for multiple types of somatic alterations, and delineated the branching architecture of clonal evolution, including the metastatic phase.

Citation Format: Bin Zhu*, Luana Poeta*, Manuela Costantini*, Tongwu Zhang*, Steno Sentinelli, Jianxin Shi, Kevin Brown, Xing Hua, Meredith Yeager, Mingyi Wang, Belynda Hicks, Stephen Chanock*, Michele Gallucci*, Vito Fazio*, Maria Teresa Landi*. Multiple region whole-genome sequencing reveals intratumor heterogeneity and branching clonal architecture of non-clear-cell renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2185.
Abstract 2186: Drug treatment induces phenotypic switch and stemness during acquisition of drug resistance
Authors: Ranganathan Santhalakshmi , Rangarajan Annapoorni
Published: August 2018

The breast tumor heterogeneity and development of drug resistance has become a challenge for anti-cancer therapy. Tumor cells acquire resistance due to intra-tumor heterogeneity imposed by epithelial to mesenchymal transition. The drugs which target epithelial cells may fail to target mesenchymal and the intermediate phenotypes due to which the cancer cells acquire drug resistance. This concept provoked us to understand the phenotypic diversity among the tumor heterogeneity which might lead to drug resistance. Hence the aim of our study is to identify the mechanisms of anti-cancer drug resistance which would ultimately help in identification of new clinical targets.

Treatment of breast cancer cell lines MCF7 and MDA MB 231 with Doxorubicin showed a loss of epithelial markers and gain of mesenchymal markers in MCF7 cells, and vice versa in MDA MB 231 cells, thereby shifting them into an intermediate phenotype. Moreover, Doxorubicin treatment of MDA MB 231-Nanog stable cells led to an increase in Nanog positive cells confirming that the treatment-induced increase in stemness property of cancer cells. We predict that phosphoproteomic dataset of the anti-cancer drug-resistant cells let us analyze the possible molecular players involved in the phenotypic switch and hence drug resistance (work in progress). Thus, our current data suggest that

the anti-cancer therapy induces cancer cells to undergo a phenotypic switch and increases the stemness property which might be responsible to gain resistance. Identification of the critical regulators of the phenotypic switch by phosphoproteomics analysis is likely to help us investigate the possible mechanisms underlying anti-cancer drug resistance. Previous reports also suggest that conventional therapies fail to eliminate cancer stem cells thereby allowing tumor relapse.

These results suggest that understanding the protein abundance and phosphorylation state of key signaling molecules would elucidate specific signaling interactions or/and pathways differentially active in drug-resistant tumors would help us predict novel kinases, and hence identify drug targets.

Citation Format: Santhalakshmi Ranganathan, Annapoorni Rangarajan. Drug treatment induces phenotypic switch and stemness during acquisition of drug resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2186.
Abstract 2212: Risk prediction for Barrett's esophagus and esophageal adenocarcinoma: Incorporation of epidemiologic risk factors and 23 confirmed genetic loci
Authors: Dong Jing , Thrift Aaron
Published: August 2018

Background & Aims: We developed comprehensive risk prediction models for Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) that incorporate a polygenic risk score (PRS) and non-genetic factors.

Methods: We used pooled data from 3,288 BE, 2,511 EAC, and 2,177 controls from BEACON, the United Kingdom Barrett's Esophagus Gene Study, and United Kingdom Stomach and Oesophageal Cancer Study. A PRS was created from 23 BE/EAC risk loci. We developed and compared risk models with various combinations of non-genetics factors and the PRS. We assessed their predictive accuracy using the area under the receiver operating characteristic curve (AUC).

Results: Individuals in the highest quartile of the PRS had 2-fold higher risks of BE (odds ratio [OR], 2.22; 95% confidence interval [CI], 1.89-2.60) and EAC (OR, 2.46; 95% CI, 2.07-2.92) compared to those in the lowest quartile of the PRS. Risk models including only demographic/lifestyle factors (age, sex, smoking, body mass index, and nonsteroidal anti-inflammatory drugs) or only gastroesophageal reflux disease (GERD) symptoms had AUCs ranging from 0.637 to 0.667. The AUCs for models adding demographic/lifestyle factors to GERD symptoms were 0.793 and 0.745 for BE and EAC, respectively. Small absolute improvement in AUCs for each model was observed when including the PRS in the model (AUCs range, 0.656-0.799). Including the PRS in the model of non-genetic factors provided 3.0% and 5.6% improvement in the net reclassification index for BE and EAC, respectively.

Conclusions: Although adding the PRS improved discrimination and net reclassification, the absolute magnitude of improvement is not sufficient to justify its clinical use.

Citation Format: Jing Dong, Aaron Thrift. Risk prediction for Barrett's esophagus and esophageal adenocarcinoma: Incorporation of epidemiologic risk factors and 23 confirmed genetic loci [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2212.
Abstract 2214: Impact of comorbidities at diagnosis on prostate cancer treatment and survival
Authors: Matthes Katarina L. , Limam Manuela , Pestoni Giulia , Held Leonhard , Korol Dimitri , Rohrmann Sabine
Published: August 2018

Background: For Switzerland, it is currently unclear in which way comorbidities influence the choice of primary treatment in prostate cancer (PCa) patients and how comorbidities affect long-term survival of PCa patients. Thus, the aim of this study was to assess the associations of comorbidities with primary treatment of PCa patients and of comorbidities with PCa-specific mortality (PCSM) compared to other-cause mortality (OCM) in Switzerland.

Patients and Methods: We included 1527 men diagnosed with PCa in 2000 and 2001 in the canton of Zurich. Comorbidities at time of diagnosis were based on the Charlson Comorbidity Index (CCI). For each patient, the scores of the respective comorbidities were summed up and classified into three groups: CCI 0 = no comorbidities, CCI 1 = sum of scores equals to 1, CCI 2+ = sum of scores equals to 2 or larger. Multiple imputation methods were applied to missing data for stage, grade and comorbidities. Multinomial logistic regression analyses were used to explore the associations of comorbidities with treatment. Cox regression models were used to estimate all-cause mortality, and Fine and Gray competing risk regression models to estimate sub-distribution hazard ratios for the outcomes PCSM and OCM.

Results: Increasing age was associated with a decreasing probability of receiving curative treatment, whereas an increasing CCI did not influence the treatment decision as strongly as age. The probability of OCM was significantly higher for patients with comorbidities compared to those without comorbidities (CCI 1: 2.07 [95% CI 1.51 - 2.85], CCI 2+: 2.34 [1.59 - 3.44]); this was not observed for PCSM (CCI 1: 0.79 [0.50 - 1.23], CCI 2+: 0.97 [0.59 - 1.59]). In addition, comorbidities had a greater impact on the patients' mortality than age.

Conclusions: The results of the current study suggest that the chronological age is a stronger predictor of treatment choices than comorbidities. This study supports the inclusion of comorbidities in treatment choices in order to offer more appropriate treatment for PCa patients to counteract over- or undertreatment.

Citation Format: Katarina L. Matthes, Manuela Limam, Giulia Pestoni, Leonhard Held, Dimitri Korol, Sabine Rohrmann. Impact of comorbidities at diagnosis on prostate cancer treatment and survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2214.
Abstract 2219: Expression of PCNA and MCM2 in ameloblastoma
Authors: Mallipudi Bhavana
Published: August 2018

Background:-Ameloblastoma is an odontogenic neoplasm with the most frequent osseous destructive lesions of the jaws. Ameloblastoma deserves special attention, because of its biological behaviour exhibiting great infiltrative potential, high recurrence rate and capacity to metastasize. The increased proliferation rate in the odontogenic epithelium can be a result of perturbations in the cell cycle regulators and dictates the aggressive behavior of the tumors. Investigating proliferative rates in the epithelial lining of these lesions helps in assessing their biological behaviour. Various cell proliferation markers are used as diagnostic and prognostic tools in oral lesions. Assessing the expression of these markers helps in estimating the proliferative index of the tissues.

Aim:- The aim of this study is to analyze the presence of, Proliferating cell nuclear antigen (PCNA) and the minichromosome maintenance-2 (MCM2) proteins, two well established markers of cell proliferation, in clinically diagnosed cases of ameloblastoma and correlate with aggressiveness and its types (Solid/multicystc{Follicular, plexiform} unicystic).

Materials and method:-14 clinically diagnosed cases of ameloblastomas (10 Solid/multicystic cases{6 cases of Follicular, 4 cases of plexiform} and 4 cases of unicystic) are obtained from the archieves of the Department of Oral and Maxillofacial Pathology to study the expression of MCM2 and PCNA. The data was analysed by Kruskals ANOVA, Mann-Whitney U test and Post hoc analysis.

Results and conclusion:- A Kruskal-Wallis ANOVA was used to detect if there was a significant difference in the expression of MCM2 and PCNA between the three variants of ameloblastoma. There was a significant difference between the three groups for mean percentage expression of MCM2 but there was uniformly higher expression of PCNA in all the three variants. Interestingly, further post hoc analysis revealed that the expression of MCM2 was significantly higher in the follicular variantas compared to the unicystic variant, suggesting that dual staining of MCM2 and PCNA may be a better marker for follicular variant.

Keywords:-Ameloblastoma, MCM2, PCNA.

Citation Format: Bhavana Mallipudi. Expression of PCNA and MCM2 in ameloblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2219.
Abstract 2249: PWS: An integrated web service platform enabling precision medicine
Authors: Duan Zhenyu
Published: August 2018

Aiming at providing an integrated platform to accelerate global drug development with personalized medicine, Predicine Web Service (PWS) is built to enable real time project status report, interpretation of clinical impact for genomic aberrations, and novel biomarker discovery with data mining algorithms and analytics.

A large-scale Predicine database is built with KnowledgeBase layer and dynamically growing genomics data layer. The KnowledBase layer integrates genome annotations, ontologies, computed variant impacts, and curated clinical implications. The dynamic genomic data layer is designed to be scalable so that both Predicine patient genomic profiles and public domain genomics data can be imported with standardized data models. A wide range of curated databases and public domain genomics profiles are integrated, including COSMIC, ClinVar, dbSNP, 1000 Genomes, ExAC, CIViC, GeneDrug KnowledgeBase, MSK IMPACT, and TCGA. Data mining algorithm and analytics are developed to enable data driven interpretation and biomarker discovery.

An intuitive web interface is developed for users to select patient space with clinical and genomics criteria, to generate patient reports with ability to drill down to multi-level variant data, and to discover biomarkers leading to hypothesis of novel targets, drug response association, and combination therapy. The project management module securely communicates the status of projects and samples for pharmaceutical companies and other clients. On PWS, private domain patient data can be combined with comprehensive public domain data for comparative and comprehensive global analysis to enable precision medicine.

Citation Format: Zhenyu Duan. PWS: An integrated web service platform enabling precision medicine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2249.
Abstract 2257: AGISTM-OncoGxKB: A simple tool for actionable genomic knowledgebase curation and clinical interpretation
Authors: Yu Pengfei , Yan Cheng
Published: August 2018

Nowadays, targeted therapy and immunotherapy have become the mainstream of cancer therapy because of their overall merit over traditional chemotherapy. With the increasing number of drug targets being discovered, cancer patients are more likely to benefit from these advanced therapies. However, the interpretation of actionable variants from patients is still a challenge in cancer clinical sequencing workflows. Here we present OncoGxKB, a crowdsource-based knowledgebase system tailored to provide clinical interpretation of variants in cancer. Based on genetic makeup of patient tumor, OncoGxKB provides actionable therapeutic strategies that maximize treatment efficacy and minimize side effects. The clinical recommendations provided cover targeted therapies, immunotherapies and clinical trials associated with actionable variants. Interpretations are rendered in tiers based on clinical evidence and stratified cancer types, following the newest AMP guideline. The crowdsource-based implementation keeps OncoGxKB comprehensive, updated, transparent and accessible to scientific community. The application programming interface (API) availability can also make the interpretation system be easily adopted to different existing pipelines. OncoGxKB is publicly available at: https://agis.admerahealth.com/OncoGxKB.

Citation Format: Pengfei Yu, Cheng Yan. AGISTM-OncoGxKB: A simple tool for actionable genomic knowledgebase curation and clinical interpretation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2257.
Abstract 2284: Semiautomated MRI segmentation workflow for glioblastoma treated by Tumor Treating Fields
Authors: Timmons Joshua J. , Lok Ed , San Pyay , Bui Kevin , Wong Eric T.
Published: August 2018

Background: Tumor Treating Fields (TTFields) therapy is an approved modality of treatment for glioblastoma. Patient anatomy-based finite element analysis (FEA) has the potential to reveal not only how these fields affect tumor control but also how they can be optimized to improve efficacy. Historically, this has been achieved with manual segmentation by an expert familiar with intracranial neuroanatomic structures, but this method is time-consuming, financially costly, and highly variable between individuals. While the availability of tools for segmenting MRIs obviates some of these obstacles, creating FEA models requires manual adjustments, including removal of disconnected voxels, incorporation of unsegmented structures that may alter the electric field, and addition of 36 electrodes matching those of the transducers on the scalp. Existing approaches are also not scalable to a large number of patient MRI scans.

Methods: Patient anatomy-based FEA models were created by segmenting MRI images—using the NewSegment algorithm from Statistical Paramedic Mapping 8 (SPM8)—into tissue “masks” using ScanIP from Simpleware (Exeter, UK). The electric properties of each tissue were applied to these masks in silico using COMSOL Multiphysics (Burlington, MA). The fidelity of the segmentations was compared using the Dice coefficient, and COMSOL generated electric field maps were compared for models with and without post-processing in ScanIP.

Results: A semiautomated workflow was developed to prepare FEA models for TTFields with fully automated electrode placement. The workflow encompassed image preprocessing, co-registration, segmentation, post-processing and mesh generation in ScanIP. Modified extended tissue probability maps were used to segment cerebellum and orbits in addition to white matter, gray matter, cerebrospinal fluid, skull, and scalp. Further automated post-processing in ScanIP cleaned up disconnected voxels, smoothed surfaces, and layered the masks to prevent erroneous boundary conditions. The Dice coefficient was greater for the model with ScanIP post-processing, as compared to the segmentations resulting from SPM8 NewSegment alone. COMSOL-generated electric field maps also displayed differences when models were generated with post-processing in ScanIP compared to those without.

Conclusions: These software and workflow may be used to accelerate the investigation of TTFields in patients by facilitating the creation of FEA models, like electric field maps, derived from patient MRI.

Citation Format: Joshua J. Timmons, Ed Lok, Pyay San, Kevin Bui, Eric T. Wong. Semiautomated MRI segmentation workflow for glioblastoma treated by Tumor Treating Fields [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2284.
Abstract 2306: Transcriptional and post-transcriptional upregulation of p27 mediates growth inhibition of isorhapontigenin/ISO on human bladder cancer cells
Authors: Xu Jiheng , Li Jingxia , Huang Chuanshu , Huang Haishan , Jiang Guosong
Published: August 2018

Our recent studies have demonstrated that Isorhapontigenin (ISO), a new derivative isolated from the Chinese herb Gnetum Cleistostachyum, effectively induces cell-cycle arrest at the G0/G1 phase and inhibits anchorage-independent cell growth through the miR-137/Sp1/cyclin D1 axis in human muscle invasive bladder cancer cells both in vitro and in vivo. Herein, we found that treatment of muscle invasive bladder cancer cells with ISO resulted in a significant upregulation of p27, a key cyclin-dependent kinase inhibitor. Importantly, knockdown of p27 caused a decline in the ISO-induced G0-G1 growth arrest and reversed ISO suppression of anchorage-independent growth in bladder cancer cells. Mechanistic studies revealed that ISO promoted p27 expression at mRNA transcription level through increasing direct binding of FOXO1 to its promoter, while knockdown of FOXO1 attenuated ISO inhibition of cell growth. On the other hand, ISO upregulated the 3'UTR activity of p27, which was accompanied by a reduction of miR-182 expression. In line with these observations, ectopic expression of miR-182 significantly blocked p27 3'UTR activity, whereas mutation of the miR-182 binding site at p27 mRNA 3'UTR effectively reversed this inhibition. Accordingly, ectopic expression of miR-182 also attenuated ISO upregulation of p27 expression and impaired ISO inhibition of cancer cell growth. Our results not only provide novel insight into understanding of the underlying mechanism related to regulation of muscle invasive bladder cancer cell growth, but also identify new roles and mechanisms underlying ISO inhibition of the growth of human bladder cancer cells.

Citation Format: Jiheng Xu, Jingxia Li, Chuanshu Huang, Haishan Huang, Guosong Jiang. Transcriptional and post-transcriptional upregulation of p27 mediates growth inhibition of isorhapontigenin/ISO on human bladder cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2306.
Abstract 2309: Increase in Cdk4 activity during progression of small intestinal neuroedocrine tumors
Authors: Contractor Tanupriya , Harris Chris R.
Published: August 2018

In the USA, there are approximately 5000 new cases of small intestinal neuroendocrine tumors (SINETs) per year, many of which already show liver metastasis upon initial diagnosis. The genetic causes of SINETs have long been a mystery. The only known recurrent mutations are in the Cdkn1b gene, which is mutated in 8% of tumors. Cdkn1b encodes p27kip1, an inhibitor of Cdk4 and Cdk2. We analyzed proteins and genes linked to the function of Cdk4 in a set of early and late SINETs (pathological stages M0 or M1). Amplification of Cdk4 activators (CcnD1, CcnD2, CcnD3), or loss of copy of Cdk4 inhibitors (Cdkn1b as well as Cdkn2a), or mutation of Cdkn1b were uncommon events, but notably occurred almost exclusively in patients with late stage disease. Patients with late stage tumors also had genetic abnormalities in Phlda3, including loss of copy, loss of heterozygosity, or presence of the rs35383942 SNP. Altogether, more than 50 percent of the advanced tumors had one or more of these genetic events, compared to less than 15 percent of the early tumors. Phlda3 is known to affect Akt activity which in turn is known to repress p27kip1 by phosphorylation, and indeed we detected more p27kip1 phosphorylation in late stage tumors. Finally, advanced tumors showed higher expression of Cdk4 and increased phosphorylation of serine-807 or serine-811 of the Rb1 protein. Together, these data argue that there is genetic pressure to increase Cdk4 activity during progression of SINETs, and suggest that patients with advanced SINETs may respond to Cdk4 inhibitors.

Citation Format: Tanupriya Contractor, Chris R. Harris. Increase in Cdk4 activity during progression of small intestinal neuroedocrine tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2309.
Abstract 2326: Time-resolved studies of necroptosis reveal distinct regulatory functions for NFκB
Authors: Metzig Marie Oliver , Mitchell Simon , Taylor Brooks , Hoffmann Alexander
Published: August 2018

Resistance to regulated cell death (RCD) is an important hallmark of cancer and reason why chemotherapy fails. Efficient reprogramming of cancer cells requires a molecular and dynamic understanding of regulatory circuits. Research has uncovered several resistance mechanisms for apoptosis with nuclear factor κB (NFκB) as a key inhibitory transcription factor. Targeted induction of necroptosis, which was recently discovered as an alternative form of RCD, could be a promising strategy to overcome apoptosis resistance. However, whether NFκB has a regulatory role in necroptosis is less clear. Here, we develop a molecular and time-resolved understanding of how NFκB regulates necroptosis. We present a real-time experimental system to quantify necroptosis in single cancer cells to study the cytotoxic effect of substances while avoiding the bias of proliferation in endpoint protocols. Using live-cell microscopy, computational cell tracking and automated image analysis we quantitate necroptotic death rates in L929 cells, a murine fibrosarcoma cell line, treated with tumor necrosis factor (TNF). While it is known that L929 cells predominantly respond with necroptosis despite rapid activation of NFκB, our experiments reveal an unsuspected temporal phasing of necroptosis over a time course of 24 hours. By perturbing NFκB activation dynamics using targeted CRISPR/Cas9 of IκB and/or Rel proteins, we find that NFκB has at least two distinct roles regulating early and late phases of TNF-induced necroptosis. Further, we will present our molecular analysis that identified NFκB-responsive candidate genes and mapped them into a functional temporo-spatial context within the NFκB-necroptosis signaling network. Our combined approach may inform novel personalized anticancer strategies to exploit targeted necroptosis while avoiding NFκB-induced drug resistance.

Citation Format: Marie Oliver Metzig, Simon Mitchell, Brooks Taylor, Alexander Hoffmann. Time-resolved studies of necroptosis reveal distinct regulatory functions for NFκB [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2326.