bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 939: Single cell mRNA expression profiling reveals heterogeneity of normal and malignant breast stem cell populations
Authors: Fouladdel Shamileh , Colacino Justin , Azizi Ebrahim , Wicha Max S.
Published: July 2017

The normal breast contains epithelial populations which are hierarchically organized, a profile recapitulated in breast cancer. At the apex of these hierarchies are "stem like" cells defined by their capacity to self-renew as well as to generate more differentiated progeny. In breast cancer these "cancer stem cells" (CSCs) have been shown to be important mediators of tumor metastasis and treatment resistance. Although the phenotypes of normal rodent and human mammary stem cells have been characterized, CSC populations are operationally defined by their capacity for tumor initiation. In addition, putative breast CSC markers such as CD44+/CD24low/- and or ALDH+ have proven useful in enriching for cells capable of tumor initiation and previous studies have suggested that these markers identify alternative mesenchymal and epithelial stem cell states, respectively. However, it remains unclear whether CSCs exist in discrete states or whether these cells actually represent a continuum reflected in heterogeneity of cell populations defined by expression of these markers. To address this question we utilized single cell mRNA expression profiling of normal and malignant breast stem cells. We first generated a panel of 96 genes representing stem cell and developmental pathways and analyzed expression of these 96 genes utilizing Fluidigm’s C1 and BioMark HD technologies and TaqMan gene expression assays. We also utilized Fluidigm’s Polaris to selectively isolate single cells that were then analyzed by illumina RNA-Seq method. Utilizing these advanced technologies, we demonstrated that both normal and malignant breast stem cells characterized by CD44+/CD24low/- and or ALDH+ expression are highly heterogeneous. For example, the ALDH isoforms ALDH1A1 and ALDH1A3 were each expressed in some single cells and co-expressed in others. ALDH1A1 expressing single cells appeared to express a unique gene pattern characterized by SLIT/ROBO, PLXNA2, RHOU and HNF1a. These results suggest that at the level of mRNA expression, normal and malignant breast stem cells display a greater heterogeneity than has previously been reported. These results have important implications for breast carcinogenesis as well as for the development of therapeutic strategies designed to target CSCs in breast cancer.

Citation Format: Shamileh Fouladdel, Justin Colacino, Ebrahim Azizi, Max S. Wicha. Single cell mRNA expression profiling reveals heterogeneity of normal and malignant breast stem cell populations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 939. doi:10.1158/1538-7445.AM2017-939
Abstract 945: Oligodendrocytes might up-regulate the Invasiveness of glioblastoma cells via angiopoietin-2 signaling
Authors: Kawashima Toshiyuki
Published: July 2017

Background & Aims: Glioblastoma (GBM, WHO Grade IV) is considered as the most lethal neoplasm of all solid cancers due to its inherent intensive invasiveness. GBM may arise de novo, or following progression from lower grade gliomas. Recently, solid tumor progression has been recognized as the product of an evolving crosstalk between the cancer cells and its surrounding glial cells. The intensive invasion activity of GBM cells might be regulated by surrounding normal cells such as oligodendrocytes or fibroblasts. In this study, we evaluated the interactive factors between GBM cells and normal glial cells to determine the role of oligodendrocytes in regulating the invasiveness of glioblastoma cells.

Methods: Two GBM cell lines, T98G and U251, were used. Two oligodendrocyte cell lines, ODC1 and ODC2, were derived one each from surgical tissues of patients with low-grade glioma (WHO Grade II). Two fibroblasts cell lines, GF1 and GF2, were derived one each from surgical tissues of patients with GBM. Oligodendrocytes and fibroblasts were confirmed by immuno-histochemical staining. The invasive property of GBM cells was analyzed in the presence or absence of conditioned medium from oligodendrocytes or fibroblasts by wound-healing assay and Boyden chamber invasion assay. The proliferation ability of GBM cells was examined by MTT assay. Subsequently Cytokine array was used to examine the cytokines and growth factors in the conditioned medium from oligodendrocytes or fibroblasts.

Results: Oligodendrocyte cells, ODC1 and ODC2 cells, significantly (p<0.01) increased the migration and invasion ability of GBM cells, T98G and U251. In contrast, fibroblasts, GF1 and GF2 cells, did not affect the migration and invasion ability of GBM cells. Cytokine array indicated that Angiopoietin-2 was found in the conditioned medium from oligodendrocytes, but not that from fibroblasts. Angiopoietin-2 significantly (p<0.01) increased the invasiveness of GBM, but not their proliferation ability.

Conclusion: Oligodendrocytes might up-regulation of the invasiveness of GBM cells via angiopoietin-2 signaling pathway. Hence, angiopoietin-2 can be considered as a promising target for the treatment of malignant gliomas.

Citation Format: Toshiyuki Kawashima. Oligodendrocytes might up-regulate the Invasiveness of glioblastoma cells via angiopoietin-2 signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 945. doi:10.1158/1538-7445.AM2017-945
Abstract 946: Characterize and identify secreted high molecular weight heparanase from PC3M conditioned medium
Authors: Ju Donghong , Kosir Mary A.
Published: July 2017

Introduction: Neutrophils, platelets, lymphocytes are typical sources of NAP-2 which is associated with heparanase activity. Heparanase degrades polymeric heparan sulfate molecules into shorter oligosaccharides, participating in extracellular matrix degradation. It is active under acidic conditions during tumor invasion and inflammatory processes. Our lab previously found that some cell lines like androgen independent prostate cancer cells (PC3M) can secrete a protein that reacts with anti-NAP-2 antibody, but has a much higher molecular weight(>50KD) than NAP-2 (MW~6-14 KD), and has heparanase activity. The purpose of this study is to characterize and identify this protein.

Procedures: Immunoprecipitation was performed using Pierce DirectIP kit according the manufacturer’s instructions. Heparin binding affinity column used HiTrap™ Heparin HP column from GE Healthcare Bio-Sciences. The binding buffer was 10mM NaAcetate pH 5.0, the eluting buffers were 0.5M-2M NaCl in 10mM NaAcetate pH 5.0. The mass spectrometry was done by KCI Proteomics Core facility.

Data: The immunoprecipitation method confirmed that this higher molecular weight protein indeed can be pulled down by the NAP-2 antibody, and after using heparin binding affinity column to purify, we can still get the > 50KD band on the western blot for NAP-2, meaning it is a heparin binding protein.

Conclusions: A protein identified with NAP-2 antibody, but with higher molecular weight than native NAP-2 is found in the conditioned medium of PC3M cells that binds heparin, further confirming a potential role in tumor progression for prostate cancer.

Citation Format: Donghong Ju, Mary A. Kosir. Characterize and identify secreted high molecular weight heparanase from PC3M conditioned medium [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 946. doi:10.1158/1538-7445.AM2017-946
Abstract 948: Characterization of the microenvironment of murine primary triple negative breast cancer
Authors: Balestrieri Kassondra , Pittman Keith , Ramez Mohamed , Vohra Nasreen , Verbanac Kathryn
Published: July 2017

The purpose of this study was to investigate the role of inflammatory cells in the metastatic process using reliably metastatic murine models of Triple Negative Breast Cancer (TNBC). We have previously selected, developed and characterized two reliably metastatic TNBC mouse models for our investigations. The T11 (claudin-low) and 2225LM (basal-like) Balb/c-derived transplantable tumors display molecular profiles that mirror human TNBC. Here we report characterization of the inflammatory cells and microenvironment in these primary TNBC tumors and at metastatic sites in both heterotopic and orthotopic models. Tumors were implanted in the s.c. flank or mammary fat pad and resected 1-2 weeks later to promote the growth of seeded metastases, when volumes reached ~700 mm3 or 300 mm3, respectively. Both flow cytometric analysis and immunohistochemistry of primary tumors demonstrated high infiltration by myeloid-derived cells (CD11b+) and low levels of lymphoid cells (CD3+). Myeloid cells were also the major infiltrating cells in lung metastases and were significantly elevated compared to normal lung. The granulocytic subset (CD11b+Ly6G+) predominated, consistent with an immunosuppressive role for cells with this phenotype (N2, G-MDSC, etc.). Primary 2225LM and T11 tumors and metastatic lung tumor homogenates were assayed for immunomodulators and compared to normal breast and lung tissue from age-matched contemporary controls. G-CSF was significantly increased in tumors and levels (pg/mg protein) were correlated with tumor burden. VEGF was significantly elevated in all tumors, as were chemoattractants for granulocytic cells (KC/CXCL1, MIP-2/CXCL2), monocytic cells (MCP-1/CCL2), eosinophils (Eotaxin/CCL11) and T cells (MIG/CXCL-9). In the heterotopic model, lung levels of KC/CXCL1 and MCP-1/CCL2 were significantly increased prior to frank lung metastasis (5-30 days post-implant). These data suggest that TNBC-derived G-CSF may play a role in the mobilization of CD11b+Ly6G+ granulocytes and progenitors from the bone marrow and key chemokines may mediate migration of these cells to metastatic sites. Future studies will define phenotypic and functional characteristics of the G-MDSC that are promoting tumor progression in these murine TNBC models.

Citation Format: Kassondra Balestrieri, Keith Pittman, Mohamed Ramez, Nasreen Vohra, Kathryn Verbanac. Characterization of the microenvironment of murine primary triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 948. doi:10.1158/1538-7445.AM2017-948
Abstract 949: Resistin potentiates stemness and chemoresistance of breast cancer cells through STAT3 activation: implications in breast cancer health disparity
Authors: Deshmukh Sachin Kumar , Bhardwaj Arun , Srivastava Sanjeev K. , Tyagi Nikhil , Al-Ghadhban Ahmed , Singh Ajay P. , Dyess Donna L. , Carter James E. , Singh Seema
Published: July 2017

Breast cancer (BC) is most frequently diagnosed cancer and remains the second leading cause of cancer-related deaths in women in the United States. African American (AA) women bear an additional burden of BC with early onset of disease, poorer prognosis, higher risk of recurrence, and worst clinical outcome as compared to Caucasian American (CA) women. Emerging evidence strongly argue the role of tumor-microenvironment (TME) in BC of AA and CA racial backgrounds. On the similar line, our earlier findings suggested that serum levels of resistin; an inflammatory cytokine are significantly elevated in AA BC patients compared to their CA counterparts. Furthermore, we demonstrated that resistin promoted growth and aggressiveness of BC cells. In the present study, we investigated the role of resistin in stemness and chemoresistance of BC cells. For this, two BC cells of CA (MDA-MB-231) and AA (MDA-MB-468) origin were treated with resistin and sphere-forming ability, a key characteristic of cancer stem cells, was determined. Data demonstrate that number of spheres is significantly enhanced in both the BC cells upon resistin stimulation. Immunoblot analyses reveal that resistin-induced sphere-forming ability is associated with enhanced levels of stemness-associated transcription factors (Nanog and KLF4) in BC cells. We next examined if resistin conferred chemoresistance to BC cells. Our data suggest that resistin-treated MDA-MB-231 and MDA-MB-468 BC cells develop greater resistance against doxorubicin-induced cytotoxicity. Notably, the effects conferred by resistin were more prominent in AA BC cells comparing to CA BC cells. Our mechanistic studies unveiled an important role of STAT3 activation in the resistin-induced stemness and chemoresistance of BC cells. Taken together, our findings provide novel insight into the role of resistin in BC biology and further strengthen its role in racially disparate clinical outcomes.

Citation Format: Sachin Kumar Deshmukh, Arun Bhardwaj, Sanjeev K. Srivastava, Nikhil Tyagi, Ahmed Al-Ghadhban, Ajay P. Singh, Donna L. Dyess, James E. Carter, Seema Singh. Resistin potentiates stemness and chemoresistance of breast cancer cells through STAT3 activation: implications in breast cancer health disparity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 949. doi:10.1158/1538-7445.AM2017-949
Abstract 950: Involvement of proinflammatory chemokine network between adipocytes and triple negative breast cancer cells
Authors: Ignacio Rosa Mistica Coles , Choi Hyeongjwa , Gibbs Carla , Lee Eunsook , Adunyah Samuel , Son Deok-Soo
Published: July 2017

Obesity has become a global epidemic and causes a chronic low-grade inflammation. This poses a large health burden because excess adiposity can lead to chronic diseases such as type 2 diabetes, cardiovascular disease and some cancers. Obese individuals get higher incidence, progression and mortality of cancers compared to lean ones. Particularly, breast cancer (BC) in women is closely associated with obesity. Despite an epidemiological link between obesity and low cancer survival rates, little is known about the molecular mechanisms by which obesity promotes BC progression. Obesity-derived chronic low-grade inflammation involves alteration of a chemokine network that may contribute to the cancer progression and metastasis. Herein, we proposed the novel concept that the chemokine network between obesity and BC builds an inflammatory burden via proinflammatory chemokines to promote cancer progression. We employed mesenchymal BC cell PY8119 and epithelial-like BC PY230 for triple negative BC (TNBC) cell model, and mouse 3T3-L1 preadipocyte and adipocyte conditioned media (CM) to mimic lean and obese conditions in vitro. We examined the profiles of chemokine signature of PY8119 and PY230 treated with preadipocytes and adipocytes CM using PCR array. Both preadipocytes and adipocytes CM-treated PY8119 and PY230 cells absent or low levels in chemokine receptors. On the other hand, the chemokines CCL2, 5, 7 and CXCL10 showed higher expression in both preadipocyte and adipocyte CM-treated PY8119. Interestingly, adipocyte CM-treated PY8119 cells dominantly expressed CXCL1-3 compared to preadipocyte CM-treated cells. In addition, CCL2, 5, 7, 20, and CXCL1, 5, 10 were highly expressed in both preadipocyte and adipocyte CM-treated PY230 cells. Moreover, CXCL2 and 3 were significantly induced in PY230 cells after treatment with adipocyte CM compared to preadipocyte CM. Taken together, the results indicate that dominant chemokines CXCL1-3 expressed in adipocyte CM-treated TNBC cells promote a pro-tumor inflammatory network. Hence, these proinflammatory microenvironment augmented by adipocytes might contribute to TNBC progression.

Citation Format: Rosa Mistica Coles Ignacio, Hyeongjwa Choi, Carla Gibbs, Eunsook Lee, Samuel Adunyah, Deok-Soo Son. Involvement of proinflammatory chemokine network between adipocytes and triple negative breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 950. doi:10.1158/1538-7445.AM2017-950
Abstract 959: Targeting neuronal activity regulated neuroligin-3 dependency for high-grade glioma therapy
Authors: Venkatesh Humsa S. , Tam Lydia T. , Woo Pamelyn J. , Monje Michelle
Published: July 2017

Neuronal activity promotes high-grade glioma (HGG) growth. An important mechanism mediating this neural regulation of brain cancer is activity-dependent cleavage and secretion of the synaptic molecule and glioma mitogen neuroligin-3 (Nlgn3), but the therapeutic potential of targeting Nlgn3 in glioma remains to be defined. Here, we demonstrate a striking dependence of HGG growth on microenvironmental Nlgn3 and determine a targetable mechanism of secretion. Patient-derived orthotopic xenografts of pediatric glioblastoma (pGBM) and diffuse intrinsic pontine glioma (DIPG) fail to grow in Nlgn3 knock out mice. Using genetic mouse models, we illustrate that Nlgn3 is cleaved from both neurons and oligodendrocyte precursor cells via the ADAM10 sheddase. Administration of an ADAM10 inhibitor robustly blocks pGBM and DIPG xenograft growth via modulation of the tumor microenvironment. This work defines the therapeutic potential of and an effective strategy for targeting Nlgn3 secretion in the glioma microenvironment, which could prove transformative for treatment of HGG.

Note: This abstract was not presented at the meeting.

Citation Format: Humsa S. Venkatesh, Lydia T. Tam, Pamelyn J. Woo, Michelle Monje. Targeting neuronal activity regulated neuroligin-3 dependency for high-grade glioma therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 959. doi:10.1158/1538-7445.AM2017-959
Abstract 96: Didhydropyrimdine dehydrogenase (DPYD) provides resistance to 5-flurouracil in mutant p53 (mtp53) expressing colorectal cancer cells
Authors: Gokare Prashanth Ravishankar , Finnberg Niklas , Dicker David , Murphy Maureen
Published: July 2017

5-Flurouracil (5-FU) is a mainstay of colorectal cancer therapy. Even though much is known about the 5-FU mechanism of action, very little is known about the genetic determinants which provide sensitivity and resistance to 5-FU. Here we provide first insights into p53, a major predictor of 5-FU response, modulating nucleotide catabolism specifically through the control of the rate limiting enzyme dihydropyrimidine dehydrogenase (DPYD). Colorectal cancer cells expressing mtp53 specifically show higher expression of DPYD as compared to the wildtype p53 (wtp53) carrying cells. Higher expression of DPYD in mtp53 cells specifically provides increased resistance to 5-FU as indicated by cellular proliferation and long term clonogenic assays. Furthermore, knockdown of DPYD in mtp53 cells preferentially resensitizes them to 5-FU as opposed to cells expressing Wtp53 by decreasing the viability and increasing apoptosis observed in these cells. Pharmacological inhibition of DPYD with gimeracil, clinical inhibitor of 5-FU phenocopies the effects seen by siRNA/shRNA mediated knockdown of DPYD. Finally, invivo studies with tumor xenograft from mtp53 carrying cells shown increase resistance to 5-FU therapy which is abrogated by stable knockdown of DPYD expression or in combination gimeracil. Preliminary analysis of TCGA patients treated with 5-FU indicate differential expression of DPYD based on specific Tp53 mutation status. Taken together our study provides first insights into crosstalk between nucleotide catabolism and mtp53 under conditions of DNA damage and metabolic stress having major implications on the therapeutic response to 5-FU the in the clinic.

Citation Format: Prashanth Ravishankar Gokare, Niklas Finnberg, David Dicker, Maureen Murphy. Didhydropyrimdine dehydrogenase (DPYD) provides resistance to 5-flurouracil in mutant p53 (mtp53) expressing colorectal cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 96. doi:10.1158/1538-7445.AM2017-96
Abstract 968: Podoplanin's diverse potential as a chemotherapeutic target for oral squamous cell carcinom
Authors: Retzbach Edward P. , Krishnan Harini , Ochoa-Alvarez Jhon A. , Shen Yongquan , Nevel Evan , Kephart David J. , Kalyoussef Evelyne , Baredes Soly , Fatahzadeh Mahnaz , Yin Kingsley , Shienbaum Alan J. , Kato Yukinari , Jensen Lasse , Goldberg Gary S.
Published: July 2017

Oral cancer is diagnosed in over 300 thousand people, and kills over 100 thousand people, around the world each year. Current treatments rely on radiation and surgery procedures that often decrease the quality of life for oral cancer survivors. There is a clear need to improve treatments for these patients. Over 90% of oral cancers are oral squamous cell carcinoma (OSCC). Most OSCC cells express the transmembrane receptor podoplanin (PDPN), which has emerged as a promising target for OSCC treatment. The PDPN receptor promotes tumor cell invasion and metastasis which leads to the vast majority of cancer deaths. Here, we describe efforts to target PDPN in order to prevent and treat oral cancer. PDPN can be targeted with Maackia amurensis seed lectin (MASL) to inhibit tumor cell migration and viability. Recent evidence also suggests that PDPN may undergo cancer specific changes, which indicates another potential route for targeting PDPN in oral cancer. Taken together, these data indicate that PDPN can serve as a functionally relevant target to prevent and combat oral cancer.

Citation Format: Edward P. Retzbach, Harini Krishnan, Jhon A. Ochoa-Alvarez, Yongquan Shen, Evan Nevel, David J. Kephart, Evelyne Kalyoussef, Soly Baredes, Mahnaz Fatahzadeh, Kingsley Yin, Alan J. Shienbaum, Yukinari Kato, Lasse Jensen, Gary S. Goldberg. Podoplanin's diverse potential as a chemotherapeutic target for oral squamous cell carcinom [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 968. doi:10.1158/1538-7445.AM2017-968
Abstract 972: Improving pre-clinical cancer pharmacogenomics with novel drug sensitivity metrics based on growth rate inhibition
Authors: Hafner Marc , Niepel Mario , Sorger Peter K.
Published: July 2017

Drug sensitivity in growing cells is conventionally quantified by IC50, AUC, or Emax values, but these metrics suffer from a fundamental flaw: they highly depend on the division rate of cell lines. This dependency creates artefactual correlations between genetic alterations and drug sensitivity which impede biomarker discovery. To address this issue, we recently developed novel drug response metrics insensitive to the number of divisions occurring during the assay. These are based on estimating growth rate inhibition (GR) under treatment using fixed assays.

Here, we illustrate the flaws of using IC50 values for pharmacogenomic studies by reanalyzing a recently published large dataset of drug sensitivity and showing cases in which differences in division rates drive associations between IC50 values and tissue type or genetic alterations. Using GR50 values prevents these artificial correlations and restores known associations between drug resistance and genomic markers such as PTEN loss driving lapatinib resistance in breast cancer cell lines. We also show how use of GRmax values, a measure of drug efficacy, allows quantifying differences in the phenotypes and distinguishing cytostatic from cytotoxic response. For drugs that have a narrow range of GR50 values like taxanes, efficacy is the most relevant metric: in many ovarian BCL2-deleted cell lines, docetaxel induces a cytotoxic response (negative GRmax values), whereas wild-type lines elicit a cytostatic response (positive GRmax values). Because efficacy (GRmax) varies independently of potency (GR50), we conclude that both metrics are complementary for pharmacogenomics and should be studied jointly.

Adopting GR metrics requires only modest changes in experimental protocols and analysis is facilitated by our interactive website: GRcalculator.org. We expect GR metrics to improve the identification of reliable drug response biomarkers and enhance the reproducibility of large-scale sensitivity studies.

Citation Format: Marc Hafner, Mario Niepel, Peter K. Sorger. Improving pre-clinical cancer pharmacogenomics with novel drug sensitivity metrics based on growth rate inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 972. doi:10.1158/1538-7445.AM2017-972
Abstract 974: Automating deconvolution of heterogeneous bulk tumor genomic data
Authors: Roman Theodore , Xiao Brenda , Schwartz Russell
Published: July 2017

Tumor heterogeneity has been linked to many measures of poor patient outcome. Despite numerous recent methodological advances, though, reliable estimates of clonal and subclonal architecture remain elusive. We present advances in computational deconvolution of tumor heterogeneity, aimed at better handling complex substructure, more automated inference, and increased flexibility to heterogeneous genomic data sources. Our methods make use of geometric models of mixture substructure, a specialized form of a strategy called manifold learning, to better resolve clonal substructure shared across genomic samples. We validate the methods on breast tumor dataset from the Cancer Genome Atlas (TCGA). We find statistically significant Spearman correlation between inferred mixture models and independently derived clinical subtype across DNA, RNA, and combined datasets. DAVID tissue term enrichment, applied to inferred amplified gene sets, further yields significant correlation (p< 0.01) with various ontological terms expected for breast tumors, for example, "Breast Carcinoma". We further verified the ability of the mixture modeling to classify tumors by progression state, showing cross-validated k-fold loss of 0.2538 in separating tumors by early (Stage I - II) vs. late (Stages III-IV) stage, corresponding to significant (p<0.001) separation by chi-squared test. The results demonstrate the effectiveness of our improved geometric deconvolution approach in resolving clonal structure to separate tumors by biologically relevant pathways and degrees of progression.

Citation Format: Theodore Roman, Brenda Xiao, Russell Schwartz. Automating deconvolution of heterogeneous bulk tumor genomic data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 974. doi:10.1158/1538-7445.AM2017-974
Abstract 981: The design and characterization of a selective TRIM24 degrader
Authors: Gechijian Lara N. , Buckley Dennis , Lawlor Matthew , Scott Thomas , Paulk Joshiawa , Reyes Jaime , Winter Georg , Erb Michael , Ott Chris , Dhe-Paganon Sirano , Bradner James
Published: July 2017

A fundamental biological understanding of the individual contributions of functional domains within multidomain proteins is critical to inform therapeutic approaches to targeting mechanisms driving human disease. TRIM24 is a multi-domain protein that has been broadly characterized as a co-regulator of transcription. It is therapeutically relevant as it is implicated as a dependency in many human cancers, however, the potent and selective inhibitors of the TRIM24 bromodomain do not have well-characterized phenotypic consequences. Where inhibition of one activity of a protein does not appear to be efficacious, chemical knockdown tools allow for the acute depletion of the entire protein, therefore eliminating all protein activities. In this study, we have used chemical degradation as one strategy to target the entire TRIM24 protein, where we have shown that a bifunctional degrader molecule hijacks the ubiquitin ligase machinery for targeted TRIM24 degradation. We have shown that TRIM24 degradation is required to perturb the oncogenic state in leukemia. In this context, TRIM24 degradation rather than bromodomain inhibition alone is required to displace TRIM24 from chromatin. Using this probe, a further understanding of the contribution of TRIM24 domains to its transcriptional activation function will provide mechanistic insight as to how TRIM24 promotes a gene expression program permissive of the oncogenic state, as well as inform a therapeutic approach to target multidomain proteins, such as TRIM24, that are tightly linked to disease.

Citation Format: Lara N. Gechijian, Dennis Buckley, Matthew Lawlor, Thomas Scott, Joshiawa Paulk, Jaime Reyes, Georg Winter, Michael Erb, Chris Ott, Sirano Dhe-Paganon, James Bradner. The design and characterization of a selective TRIM24 degrader [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 981. doi:10.1158/1538-7445.AM2017-981
Abstract 99: Identify potential kinetochore protein inhibitors to overcome cisplatin resistance
Authors: Yin-Ju Chen , Chiou Jeng-Fong
Published: July 2017

Cisplain is the most commonly used chemotherapeutic drug for cancer, while the resistance causes treatment failure. Cisplatin resistance may involve in many molecular changes so identify aberrations in cisplatin-resistant (CR) genes and find new therapeutic strategies could provide valuable information to reduce therapeutic resistance. The aim of this study is to search CR genes and identify potential novel drugs to overcome cisplatin resistance. To identify aberrations in CR genes, three CR genetic signatures were collected and analyzed differential expression genes from lung, ovarian and oral cancer cells. After integration of CR signatures, the kinetochore associated proteins, including NUF2, SPC25, PC24, DSN1, SKA2, KNTC1, MIS18A and SKA1 were up-regulated in various CR cells. Silencing of kinetochore associated proteins increased cisplatin sensitivity. For identification of kinetochore associated protein inhibitors to overcome cisplatin resistance, CR signatures were queried to the Connectivity map (Cmap) database to search for potential drugs which may reverse cisplatin resistance. 3 compounds exhibited cytotoxicity effect on the cisplatin-resistant cells and reduced kinetochore associated proteins expression level. Taking together, this study demonstrates kinetochore associated proteins participate in cisplatin resistance and identify potential inhibitors to overcome cisplatin resistance.

Citation Format: Chen Yin-Ju, Jeng-Fong Chiou. Identify potential kinetochore protein inhibitors to overcome cisplatin resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 99. doi:10.1158/1538-7445.AM2017-99
Abstract 994: Diagnosing leukemia structural variations via a novel genome mapping approach
Authors: Pool Christopher , Xu Jie , Bann Darrin , Goldenberg David , Sharma Arati , Claxton David , Yue Feng , Broach James
Published: July 2017

Identification of structural variants (SVs) is critical to the prognosis of AML. SVs are not readily identified by next generation sequencing methods and are currently diagnosed by cytogenetics, an intrinsically low resolution tool. We have adapted a new method for determining large SVs as a clinical tool for evaluating AML and other cancer genomes. The Bionano Irys images in microfluidic nanochannels large (>150 Kb) segments of genomic DNA that have been bar coded by site specific nicking and local incorporation of fluorescent label. The complement of individual molecules can be assembled through matching bar codes to create a de novo map of the genome from which, by matching to a reference genome, identifies and catalogs structural variants at resolution of ca. 1 Kb.

With this technology, we characterized structural variants signatures in breast cancer, renal clear cell carcinoma, and CML cell lines. Structural variants were then validated via PCR/Sanger sequencing, fluorescent in situ hybridization and whole genome sequencing. We identified a thorough compendium of consistent false positive rearrangements identified by this technology, most of which reflect errors in the reference human genome assembly. We then applied this methodology to ten AML patient samples, seven from archived blood samples and three directly obtained from newly diagnosed patients. Karyotyping on one archived sample identified a t(6:9) translocation in the majority of cells. We identified that rearrangement at a much higher resolution than cytogenetics, which allowed us to map the breakpoint via PCR/Sanger sequencing to nucleotide resolution and confirm a fusion of NUP214 to DEK, a known oncogene. We also discovered the reciprocal t(9:6) translocation, which had not been identified by cytogenetics. In the six other cases from archived samples, we have confirmed the translocation identified by cytogenetic karyotyping and in several cases found additional rearrangements. Moreover, in the first pediatric case, which we completed within five days of obtaining the sample, we have identified four distinct translocations, all of which have been associated previously with AML.

Overall, this is technology has the ability to quickly and accurately identify SVs in cancer cell lines and AML patient samples with higher resolution than cytogenetics, demonstrating its clinical usefulness in the diagnosis and subsequent treatment of leukemia.

Citation Format: Christopher Pool, Jie Xu, Darrin Bann, David Goldenberg, Arati Sharma, David Claxton, Feng Yue, James Broach. Diagnosing leukemia structural variations via a novel genome mapping approach [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 994. doi:10.1158/1538-7445.AM2017-994
Abstract CT051: Tumor treating fields in pediatric recurrent high-grade glioma and ependymoma
Authors: Goldman Stewart , Onar-Thomas Arzu , Dunkel Ira , Hwang Eugene
Published: July 2017

Background

Recurrent or progressive pediatric CNS tumors have a poor prognosis under current treatment regimens. For children with high-grade gliomas (HGG), once progression occurs, most patients cannot be cured, and median survival remains < 1-2 years; overall survival of recurrent/progressive ependymoma is also poor in children. Tumor Treating Fields (TTFields) is an anti-mitotic cancer therapy for the treatment of recurrent (supratentorial) glioblastoma (GB).) A phase 3 clinical trial comparing TTFields monotherapy with physician’s choice chemotherapy in adult patients with recurrent GB demonstrated comparable overall survival and improved quality of life. In this multicenter feasibility trial we plan to examine the feasibility and device-related toxicity of TTFields in children with supratentorial HGG and ependymoma. The secondary objectives include: response rate, Event-Free Survival, compliance on use of device and Quality of Life (QoL) of tehe children (aged 8+) and families.

Methods

The Optune device will be worn ≥ 18 hours/day for at least 23 days out of 28 days of cycle one. Patients will have Brain MRI with and without contrast performed prior to therapy, after cycles 2, 4, 6, 9, then every 3 cycles thereafter until time of progression or completion of treatment. For those patients who complete at least 9 cycles of therapy, an MRI will be performed every 3 cycles for 2 years then every 4 months after completion of treatment.Treatment may continue up to 26 cycles pending observed benefit and safety. A sample size of 20 patients is needed with an interim analysis conducted after the first 11 patients. Kaplan-Meier estimates of EFS for all eligible patients who use the device for < 1 day will be provided separately for the HGG and Ependymomahistology-based cohorts. We will also estimate the rates of confirmed sustained objective responses (CR+PR) observed during treatment. All PROMIS and Neuro-QoL scores will be reported using T-score matrix (mean=50 and SD=10). The projected accrual rate is 1.5-2.5 patients per month. Patients will be followed for 2 years.

Citation Format: Stewart Goldman, Arzu Onar-Thomas, Ira Dunkel, Eugene Hwang. Tumor treating fields in pediatric recurrent high-grade glioma and ependymoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr CT051. doi:10.1158/1538-7445.AM2017-CT051
Abstract CT061: Novel safety of high dose ascorbic acid and induction chemotherapy for high risk pancreatic cancer
Authors: Bruckner Howard W. , Hirschfeld Azriel , Gurell Daniel , Lee King
Published: July 2017

Background: High dose ascorbic acid has been reported to have in vitro anticancer activity. Low dose combination chemotherapy with GFLIP (gemcitabine, 5fu, leucovorin, irinotecan, oxaliplatin) is an effective regimen for patients with pancreatic cancer. Combining high dose ascorbic acid with GFLIP may be a synergistic and well tolerated treatment regimen.

Methods: High dose ascorbic acid with a range of 75-100 grams IV given on an average 1-2 times per week was combined with GFLIP given on a 2 week schedule for patients with pancreatic cancer. Eligibility criteria include locally advanced, unresectable, recurrent and metastatic disease. Patients who progressed on prior treatment, ECOG 0-2, were also included. There was no age cut off.

Results: 26 patients were treated, 9 patients were ≥ 70 years of age (35%). 25 out of 26 patients had stage IV disease (96%). Nine out of 26 patients had received at least one prior chemotherapy regimen (35%). Five out of 26 patients had a grade 3 neutropenia (19%) there was no grade 4 neutropenia. One out of 26 patients (4%) had a grade 3 anemia and thrombocytopenia. There was no neutropenic fever and no limiting gastrointestinal (diarrhea, stomatitis) toxicity. This study included patients with a performance status of 2, patients who had progressed on prior chemotherapy and older patients.

Conclusion: High dose ascorbic acid combined with GFLIP chemotherapy is a safe and well tolerated treatment regimen for high risk patients with pancreatic cancer. This level of safety justifies the further study of this treatment regimen especially for high risk patients who would not be eligible for standard high dose combination chemotherapy in pancreatic cancer.

Citation Format: Howard W. Bruckner, Azriel Hirschfeld, Daniel Gurell, King Lee. Novel safety of high dose ascorbic acid and induction chemotherapy for high risk pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr CT061. doi:10.1158/1538-7445.AM2017-CT061
Abstract CT078: Impact of disease burden and transplant on long-term survival after CD19 CAR therapy in adults with relapsed B-cell acute lymphoblastic leukemia
Authors: Park Jae H. , Rivere Isabelle , Wang Xiuyan , Senechal Brigitte , Curran Kevin , Sauter Craig , Wang Yongzeng , Santomasso Bianca , Li Daniel , Brentjens Renier , Sadelain Michel
Published: July 2017

Objectives: CD19-specific chimeric antigen receptor (CAR) T cells have demonstrated high initial responses in patients with relapsed B-cell acute lymphoblastic leukemia (B-ALL). However, clinical characteristics associated with the durability of response remain undefined. Herein, we report the results from analysis of our phase I clinical trial of 19-28z CAR T cells in adult patients with relapsed B-ALL with a focus on impact of pre-treatment disease burden and post-CAR T cell allogeneic transplant on long-term clinical outcome.

Methods: Adults with relapsed B-ALL were infused with autologous T cells expressing the 19-28z CAR. Disease burden was assessed by bone marrow biopsy immediately prior to T cell infusion. We grouped patients into 2 cohorts based on disease burden upon T cell infusion: minimal residual disease (MRD) with <5% blasts in bone marrow and morphologic disease (≥5% blasts). Median follow-up duration was 18 months (range, 0.2-57.3).

Results: 51 adults received 19-28z CAR T cells; 20 in the MRD and 31 in the morphologic cohort. Complete remission (CR) rates were comparable (95% and 77%, respectively). However, median event-free and overall survivals widely diverged among the 42 patients who achieved MRD-negative CR: not reached (NR) (95% confidence interval [CI]: 4.2-NR) vs. 6.3 months (95% CI, 4.8-9.0) (p=0.0005), and NR (95% CI, 15.3-NR) vs. 17 months (95% CI, 8.5 - 36.2) (p=0.0189), in the MRD and morphologic cohorts, respectively. Subsequent allogeneic HSCT in either cohort did not improve survival (p=0.8). MRD cohort patients developed substantially less severe cytokine release syndrome (CRS) and neurotoxicity, both correlating with peak CAR T cell expansion (p=0.0326 and p=0.0001, respectively).

Conclusion: Despite comparable initial CR rates between the two cohorts, durability of 19-28z CAR T cell mediated remissions and survival in adult patients with relapsed B-ALL positively correlated to a low disease burden and do not appear to be enhanced by allogeneic transplant. Our findings strongly support the early incorporation of CD19 CAR therapy before morphologic relapse in B-ALL.

Citation Format: Jae H. Park, Isabelle Rivere, Xiuyan Wang, Brigitte Senechal, Kevin Curran, Craig Sauter, Yongzeng Wang, Bianca Santomasso, Daniel Li, Renier Brentjens, Michel Sadelain. Impact of disease burden and transplant on long-term survival after CD19 CAR therapy in adults with relapsed B-cell acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr CT078. doi:10.1158/1538-7445.AM2017-CT078
Abstract CT080: Pharmacokinetic and pharmacodynamic analysis of M7824, a dual anti-PD-L1 and TGFβ TRAP molecule, in the first-in-human phase I dose escalation study
Authors: Cao Liang , Kang Zhigang , Li Linghui , Strauss Julius , Dussault Isabelle , Gulley James
Published: July 2017

Introduction: M7824 is a bifunctional molecule that blocks both PD-L1 and TGFβ1-3. In this first-in-human phase I dose escalation study, in addition to monitoring the pharmacokinetics of M7824, we aimed to confirm its mechanism of action, particularly against the TGFβ cytokines.

Methods: Patients were treated with M7824 intravenously at 5 dose levels of 0.3, 1, 3, 10, and 20 mg/kg every two weeks. PK analyses were performed from samples up to day 85 (7th dose). PD-L1 target occupancy was measured in CD3+ PBMCs by flow cytometry from patient blood collected at pre-dose, Day 2 (D2), D15, and D43. Further, the blood levels of TGFβ1-3 and pro-inflammatory cytokines were measured at these time points with an additional time point at D8 using analytically validated Luminex bead- and ECLIA-based multiplex immunoassays.

Results: Results indicated a half-life of 4-8 days for M7824, which increased with dose up to 3 mg/kg, and was subsequently dose independent at dose levels of > 3 mg/kg. M7824 PK exposure during the first cycle increased in an approximately dose-proportional manner between 3 to 20 mg/kg, without significant accumulation within the first 85 days of treatment. There was PD-L1 target occupancy plateaued at about 80% for dose levels 3-20 mg/kg which was maintained throughout the dosing interval. Furthermore, there was a small (1.7 fold on D2) but significant induction of IFNγ at 0.3-20 mg/kg (p=0.001, n=19). TGFβ1-3 blood levels were reduced by a minimum of 99%, 92%, and 91%, respectively, at all time points for dose levels 1-20 mg/kg. At the dose of 0.3 mg/kg, TGFβ1-3 levels were depleted at D2 and D8, but not at D15 with an average reduction of 63%, 42% and 67%, respectively. Moreover, there was a correlation between the drug PK levels and the TGFβ trapping. Thus, TGFβ1-3 trapping was achieved in the circulation at drug dose level of 1 mg/kg and above.

Conclusion: This study demonstrates in vivo evidence for highly significant trapping (>90%) of circulating TGFβ molecules (β1, β2, β3) by the bifunctional agent M7824 at dose levels of 1 mg/kg and higher, in addition to its high degree of peripheral PD-L1 target occupancy (80%). Further studies to evaluate the PK/PD, safety, and efficacy profile of M7824 are ongoing.

Citation Format: Liang Cao, Zhigang Kang, Linghui Li, Julius Strauss, Isabelle Dussault, James Gulley. Pharmacokinetic and pharmacodynamic analysis of M7824, a dual anti-PD-L1 and TGFβ TRAP molecule, in the first-in-human phase I dose escalation study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr CT080. doi:10.1158/1538-7445.AM2017-CT080