bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB-189: Pharmacological reactivation of MYC-dependent apoptosis cooperates with anti-PD1 immunotherapy
Authors: Haikala Heidi M. , Anttila Johanna M. , Savelius Mariel , Marques Elsa , Raatikainen Tiina , Ilander Mette , Hakanen Henna , Mattson Johanna , Heikkila Paivi , Leidenius Marjut , Joensuu Heikki , Mustjoki Satu , Kovanen Panu , Eilers Martin , Leverson Joel D. , Klefström Juha T.
Published: August 2019

Elevated MYC levels sensitize tumor cells to apoptosis but the therapeutic potential of this mechanism remains unclear. We find, in a model of MYC-driven breast cancer, that pharmacological activation of AMPK dramatically synergizes with BCL-2/BCL-XL inhibitors to activate MYC-dependent apoptosis. We demonstrate the translational potential of an AMPK and BCL- 2/BCL-XL co-targeting strategy in ex vivo and in vivo models of MYC-high breast cancer. Metformin combined with either navitoclax or venetoclax efficiently inhibits tumor growth, confers survival benefits and induces tumor infiltration by immune cells. However, withdrawal of the drugs allowed tumor re- growth with presentation of PD1+/CD8+ T cell infiltrates, suggesting immune escape. A two-step treatment regimen, beginning with neoadjuvant metformin+venetoclax to induce apoptosis and followed by tumor resection and adjuvant metformin+venetoclax+anti-PD1 treatment to overcome immune escape, led to durable antitumor responses even after drug withdrawal. We demonstrate that pharmacological reactivation of MYC-dependent apoptosis is a powerful antitumor strategy involving both tumor cell depletion and immunosurveillance.

Citation Format: Heidi M. Haikala, Johanna M. Anttila, Mariel Savelius, Elsa Marques, Tiina Raatikainen, Mette Ilander, Henna Hakanen, Johanna Mattson, Paivi Heikkila, Marjut Leidenius, Heikki Joensuu, Satu Mustjoki, Panu Kovanen, Martin Eilers, Joel D. Leverson, Juha T. Klefström. Pharmacological reactivation of MYC-dependent apoptosis cooperates with anti-PD1 immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-189.
Abstract LB-202: Immunotherapy with TMV vaccine inhibits metastatic tumor growth in an immune checkpoint resistant murine lung cancer model
Authors: Huang Haley Lei , Bommireddy Ramireddy , Munoz Luis E. , Menon Ashwathi P. , Ramalingam Suresh , Selvaraj Periasamy
Published: August 2019

Lung cancer is the second most common cancer among men and women and the leading cause of cancer deaths in the world. Despite the advancements in diagnostic technologies and the development of novel treatments in the recent years such as immune checkpoint inhibitor (ICI) therapy, the prognosis of lung cancer patients is still poor, and the survival rate is low. The patient-to-patient heterogeneity is the major problem in treating lung cancer, which results in differential responses to ICI therapy. In this study, we investigated the efficacy of a vaccine immunotherapy prepared by modification of tumor membrane vesicles (TMVs) prepared from the tumors to express immunostimulatory molecules in combination with ICI therapy in a partially ICI resistant murine lung cancer model. We demonstrate that prophylactic vaccination of TMV adjuvanted with immunostimulatory molecules prevents the CMT-167 tumor growth in mice and helps the mice develop immunological memory to the tumor cell challenge. In a therapeutic setting, the TMV vaccine inhibited tumor growth and induced primary tumor regression in 40% of mice and significantly reduced the metastatic tumor burden. However, the combination of TMV vaccination with anti-PD-1 mAb doesn’t have a synergistic or additive effect on the primary or metastatic tumor growth. Overall, these studies provide insight into using the TMV vaccine immunotherapy for treating lung cancer.

Funding: Supported by the Lung Cancer seed grant from the Winship Cancer Institute of Emory University

Citation Format: Lei Huang, Dr. Selvaraj's lab. Immunotherapy with TMV vaccine inhibits metastatic tumor growth in an immune checkpoint resistant murine lung cancer model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-202.
Abstract LB-204: DNA vaccine co-expressing Her2/ErbB2 antigen, fused with LAMP, elicits strong antitumor effects in vivo by increasing tumor infiltration with CD8+ T cells
Authors: Xu Renhuan , Heiland Teri
Published: August 2019

DNA vaccines have emerged as an attractive immunotherapeutic approach against infectious diseases and cancer due to its fast, efficient design and validation. It remains, however, a challenge in clinical settings due to historically low levels of immunogenicity in humans. In order to enhance the immunogenicity of DNA vaccines used as a cancer therapy, we have developed a nucleic acid platform, UNITE (UNiversal Intracellular Targeted Expression), which combines novel delivery methods and adjuvants which complement our lysosomal targeting technology. Fusing a tumor associated antigen (TAA) with the Lysosomal Associated Membrane Protein 1 (LAMP-1), we can activate Ag specific CD4+ T cells by targeting the major histocompatibility complex II compartment. In this study, we selected ErbB2/Her2 as the cancer target because it is a broadly overexpressed and well-characterized oncoantigen.

Mice vaccinated with Her2-LAMP DNA demonstrate robust Her2-specific CD4+ and CD8+ T cells, in addition to antibody responses, which in turn have significant antitumor effect in murine breast and bladder tumor models. Moreover, we demonstrate that the Her2-LAMP vaccine promotes CD8+ T cell tumor infiltration to a greater degree than when compared to a traditional DNA vaccine without LAMP. In summary, we show that UNITE as a nucleic acid platform, can enhance antitumor immunity in vivo.

Citation Format: Renhuan Xu, Teri Heiland. DNA vaccine co-expressing Her2/ErbB2 antigen, fused with LAMP, elicits strong antitumor effects in vivo by increasing tumor infiltration with CD8+ T cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-204.
Abstract LB-236: Genomic characterization of circulating tumor cells in de novo metastatic prostate cancer
Authors: Chai Shoujie , Malihi Paymaneh D. , Apariciop Ana M. , Chapin Brian F. , Lin Matthew , Storgard Ryan , Velasco Carmen Ruiz , Kolatkar Anand , Hicks James , Kuhn Peter
Published: August 2019

Background: The absence of biomarkers that identify clinically meaningful biological subsets of prostate cancer results in the homogeneous application of systemic therapies to a heterogeneous disease and hampers therapy development. This heterogeneity may become more evident at the molecular level under the pressure of androgen withdrawal. Here, we longitudinally characterized peripheral blood circulating tumor cells (CTCs) from patients with de novo metastatic prostate cancer to examine the phenotypic and genomic changes induced by androgen suppression.

Methods: Peripheral blood samples were collected at MD Anderson Cancer Center from a cohort of DNM1PCa patients under clinical trial NCT01751438. Timepoints of collection includes baseline (BSL, before treatment) and 6 months (6mo, after 6 months of systemic therapy). We used the High-Definition Single Cell Assay (HD-SCA) workflow for CTC enumeration, morphology (nuclear size, DAPI intensity, cytokeratin (CK), androgen receptor (AR) intensity and genomics (whole-genome copy number aberration analysis) evaluation. This workflow utilizes an enrichment-free fluorescence based (DAPI/ CK/ CD45/ AR) CTC identification system and single-cell genomic sequencing.

Results: Twenty-nine of the 58 available blood samples contained CTCs: 15 of the 28 (53.6%) collected at BSL (median 2.00 CTCs/mL, range 0.84-74.15) and 14 of the 30 (46.7%) collected at 6mo (median 2.43 CTCs/mL, range 0.96-13.85). However, at the 6mo timepoint, the CTCs had undergone a significant morphological shift in nuclear area local ratio (BSL vs 6mo: 1.036 vs 1.165, p=0.039), DAPI intensity (0.199 vs 1.030, p=0.036), CK intensity (18.978 vs 15.651, p=0.006), AR intensity (0.681 vs -0.468, p=0.037) and AR+ percentage (36.25% vs 15.38%, p=0.020). Further, genomic analysis of two patients at BSL indicated copy number aberrations including PTEN, TP53, RB1 and BRCA2 loss and MYC gain.

Discussion: This study aims at characterizing changes induced by systemic therapies in CTC potential biomarkers that identify distinct subsets of disease biology. The changes observed in patient subsets may serve as clinically relevant biomarkers to optimize treatment and improve prognosis.

Citation Format: Shoujie Chai, Paymaneh D. Malihi, Ana M. Apariciop, Brian F. Chapin, Matthew Lin, Ryan Storgard, Carmen Ruiz Velasco, Anand Kolatkar, James Hicks, Peter Kuhn. Genomic characterization of circulating tumor cells in de novo metastatic prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-236.
Abstract LB-252: Group-based smoking cessation treatment for incarcerated men: A pilot study
Authors: Valera Pamela , Acuna Nicholas
Published: August 2019

Introduction. Cigarette smoking is the leading cause of morbidity and mortality that contributes to over six million deaths worldwide and is projected to cause more than eight million deaths per year by 2030. Overall cigarette smoking rates in the United States (U.S.) is estimated at 14%, but this number increases to 50-83% of smokers within correctional populations.

Methods. Using a cohort study design, sixteen incarcerated male smokers from a Northeastern state maximum prison facility in the U.S. participated in a 4-week group-based smoking cessation treatment program with nicotine replacement therapy and a one-month follow-up period to determine quit behaviors and abstinence. The goal of this pilot study was to explore the feasibility, acceptability, and efficacy of a smoking cessation group treatment intervention for incarcerated smokers where tobacco products are permitted.

Results. In this feasibility study, the average age of participants enrolled was 43 (SD = 13.69), and their first incarceration was at 19 (SD = 7.30). The majority of the participants identified as African American/Black (62.5%), 31.3% identified as Caucasian/White, and 6.3% identified as Hispanic/Latino as their race/ethnicity. The average age where individuals started smoking was 13.8 (SD = 3.2) and the total number of years smoked is 25.6 (SD = 14.9). The mean of cigarettes smoked each day was 13.0 (SD = 9.8). More than half of the people in the study indicated that they relight their cigarettes. Additionally, the two brands that participants indicated as their favorite were Kite (18.8%) and Newport (68.8%). Of all the participants, 87.5% indicated that they smoked menthol cigarettes. Majority of the participants indicated the importance of quitting tobacco (8.80 ± 1.82) and that they had a very difficult time during their previous quit attempts (43.8%). Previous quit attempts included forced abstinence while in solitary confinement or administrative segregation. At the 4-week follow up period, half of the participants that were enrolled in the group-based smoking cessation treatment and completed the program indicated that they did not smoke or use tobacco in the past 7-days or since their initial quit date (50.0%).

Conclusion. Group-based smoking cessation treatment should be prioritized as an effective intervention to aid incarcerated smokers to quit smoking. This study builds upon our growing knowledge of tobacco dependence and smoking cessation treatment, with a focus on individuals involved in the criminal justice system.

Citation Format: Pamela Valera, Nicholas Acuna. Group-based smoking cessation treatment for incarcerated men: A pilot study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-252.
Abstract LB-255: Acquired and intrinsic resistance to vemurafenib in BRAFv600e-driven melanoma brain metastases
Authors: Gooijer Mark C. de , Zhang Ping , Buil Levi C. , Freriks Stephan , Li Gang , Beijnen Jos H. , Tellingen Olaf Van
Published: August 2019

Purpose: BRAFV600-mutated melanoma brain metastases (MBMs) are generally responsive to BRAF and MEK inhibitors, albeit that responses are generally less durable than of extracranial metastases. We have studied the impact of the drug efflux proteins P-glycoprotein (P-gp; ABCB1) and breast cancer resistance protein (BCRP; ABCG2) at the blood-brain barrier (BBB) on the efficacy of vemurafenib against BRAF-mutated A375 MBMs.

Experimental design: We have implanted BRAF-mutated A375 tumor cells in the brains of wildtype and Abcb1a/b;Abcg2-/- mice. We characterized the BBB in the tumors, treated the mice with oral vemurafenib, analyzed drug levels in plasma and brain lesions and determined the efficacy in brain metastases and subcutaneous lesions.

Results: Although A375 MBMs disrupt the integrity of the BBB, as shown by contrast-enhanced MRI, vemurafenib achieves greater antitumor efficacy in Abcb1a/b;Abcg2-/- mice compared to wild-type mice. P-gp and BCRP in brain tumor vessels limit vemurafenib penetration into A375 MBMs. Vemurafenib efficacy in both strains was similar against subcutaneous A375 tumors. Intriguingly, although initially responsive, A375 MBMs rapidly developed therapy resistance, even in Abcb1a/b;Abcg2-/- mice, and this was unrelated to pharmacokinetic or target inhibition issues. Rather, MBMs likely resorted to non-canonical growth signaling, as target inhibition of canonical MAPK and PI3K pathway signaling components was maintained in resistant intracranial A375 tumors.

Conclusions: In line with clinical data, BRAFV600E-positive MBMs are less responsive to vemurafenib. This is partly due to protection by the BBB, but also because they rapidly acquire further resistance by resorting to non-canonical growth signaling.

Citation Format: Mark C. de Gooijer, Ping Zhang, Levi C. Buil, Stephan Freriks, Gang Li, Jos H. Beijnen, Olaf Van Tellingen. Acquired and intrinsic resistance to vemurafenib in BRAFv600e-driven melanoma brain metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-255.
Abstract LB-256: PDGFRβ blockade bypasses resistance to combined MEK1/2-JAK2 inhibition in triple-negative breast cancer via intratumoral CD8+ T-cells infiltration
Authors: Kalimutho Murugan , Khanna Kum Kum
Published: August 2019

Despite the increasing progress in breast cancer research, currently there is no targeted therapy available for TNBC. Here, we demonstrated a novel resistance mechanism mediated by PDGFRβ in TNBC cells. We showed that TNBC cells exposed to JAK2 or MEK1/2 inhibitors promote PDGFRβ upregulation. Using publically available databases, we found that basal-like breast cancer patients expressing high PDGFRβ exhibit poor relapse-free survival. We found that JAK2 overexpression controls PDGFRβ protein degradation. Blockade of PDGFRβ with JAK2 and MEK1/2 inhibitors significantly impacted the CD44+/CD24- stem-cell-like cells and the growth of basal-like breast cancer xenografts in vivo through intratumoral CD8+ T cells in a manner that is reversed by anti-CD8 antibody treatment. Together, these findings reveal a novel regulatory role of JAK2-mediated PDGFRβ proteolysis and provide an example of a PDGFRβ-mediated resistance mechanism upon JAK2 and MEK1/2 inhibition in TNBC.

Citation Format: Murugan Kalimutho, Kum Kum Khanna. PDGFRβ blockade bypasses resistance to combined MEK1/2-JAK2 inhibition in triple-negative breast cancer via intratumoral CD8+ T-cells infiltration [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-256.
Abstract LB-262: Targeting of the PI3K/AKT pathway overcomes enzalutamide resistance by inhibiting the induction of glucocorticoid receptor
Authors: Adelaiye-Ogala Remi M. , Kelly Kathleen , VanderWeele David
Published: August 2019

Background: An evolving concept that contributes to the understanding of resistance to androgen deprivation therapy and/or androgen receptor (AR) antagonist in prostate cancer is the ability of the cells to bypass AR blockade and turn on compensatory hormone signaling for survival. Recent preclinical and clinical studies demonstrate that induction of GR expression confers resistance to AR-targeted therapy. Hence therapeutic strategies to overcome GR-mediated resistance are warranted.

Experimental Design: Prostate cancer cell-lines and patient derived xenograft (PDX) models were exposed to the pan-AKT inhibitor ipatasertib or other PI3K/AKT- pathway inhibitors with or without AR blockade. AR and GR array determined differentially expressed AR/GR target genes. Protein expression levels were measured. Cell viability and tumor growth was determined in response to treatment.

Results: AKT inhibitor as monotherapy significantly decreases cell viability across multiple prostate cancer models. The cytotoxic effect is enhanced by AR inhibition and is most pronounced in models that induce compensatory GR expression. The pan-AKT inhibitor ipatasertib as well as other inhibitors of the PI3K/AKT pathway decreased GR activity through AR-dependent and AR-independent mechanisms. Importantly, AKT inhibition, with and without AR blockade, demonstrated significant anti-tumor activity in several in vivo prostate cancer models with no noticeable toxicity.

Conclusion: Inhibition of the PI3K/AKT pathway blocks GR activity and overcomes GR-mediated resistance to AR-targeted therapy. This therapeutic approach has immediate clinical relevance as ipatasertib is currently in advanced clinical development and provides a supportive tool for how to manage patients with acquired resistant to AR-targeted therapy.

Citation Format: Remi M. Adelaiye-Ogala, Kathleen Kelly, David VanderWeele. Targeting of the PI3K/AKT pathway overcomes enzalutamide resistance by inhibiting the induction of glucocorticoid receptor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-262.
Abstract LB-274: Identification and characterization of LY3410738, a novel covalent inhibitor of cancer-associated mutant Isocitrate Dehydrogenase 1 (IDH1)
Authors: Brooks Nathan , DeWalt Robin , Boulet Serge , Lu ZhaoHai , Kays Lisa , cavitt Rachel , Gomez Sandra , Strelow John , Milligan Paul , Roth Kenneth , Bauer Renato , Antonysamy Stephen , Hahn Patric , Rankovic Zoran , McCann Denis , Mo Gary , Tiu Ramon , Burkholder Timothy , Geeganage Sandaruwan , Gilmour Raymond
Published: August 2019

Somatic gain-of-function mutations in IDH1 have been identified in multiple tumor types including AML, glioma, cholangiocarcinoma and chondrosarcoma. The neo-enzymatic activity of mutant IDH1 results in accumulation of the oncometabolite 2-hydroxyglutarate (2-HG), leading to a hyper-methylation phenotype, a block in cell differentiation, and tumor growth. Using a structure-based drug design approach, we have developed a highly potent covalent inhibitor of mutant IDH1. LY3410738 modifies a single cysteine (Cys269) in the allosteric binding pocket and rapidly inactivates the enzyme with a KI/Kinact = 84,257 M-1sec-1. The compound selectively inhibits the 2-HG in IDH1 mutant tumor cells without depleting the levels of a-ketoglutarate. Using patient-derived primary AML cells, we demonstrated that LY3410738 was more potent than AG120 in reversing the block in differentiation associated with IDH1 mutant activity. In vivo, LY3410738 displayed prolonged pharmacodynamic activity, depleting 2-HG levels in tumors at low circulating exposures and for an extended time after clearance of compound. Importantly, LY3410738 has the ability to cross the blood-brain barrier and can achieve concentrations in the brain that exceed those needed to engage the target. Consistent with this, LY3410738 effectively inhibits 2HG in orthotopic glioma models. Using patient-derived IDH1 mutant orthotopic AML models, we demonstrated that LY3410738 effectively inhibited 2-HG, induced differentiation, and cleared AML from mice. Collectively, LY3410738 represents the first covalent brain-penetrant mutant IDH1 inhibitor with potential for Best-in-Class activity.

Citation Format: Nathan Brooks, Robin DeWalt, Serge Boulet, ZhaoHai Lu, Lisa Kays, Rachel cavitt, Sandra Gomez, John Strelow, Paul Milligan, Kenneth Roth, Renato Bauer, Stephen Antonysamy, Patric Hahn, Zoran Rankovic, Denis McCann, Gary Mo, Ramon Tiu, Timothy Burkholder, Sandaruwan Geeganage, Raymond Gilmour. Identification and characterization of LY3410738, a novel covalent inhibitor of cancer-associated mutant Isocitrate Dehydrogenase 1 (IDH1) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-274.
Abstract LB-276: Farnesyltransferase inhibitor (FTI)-induced growth inhibition of HRAS-mutant head and neck cancers is enhanced by concurrently inhibiting compensatory upregulation of the ERK-MAPK kinase cascade
Authors: Javaid Sehrish , Nguyen Victoria V. , Waters Andrew M. , Goodwin Craig M. , Der Channing J. , Cox Adrienne D.
Published: August 2019

Activating mutations in the HRAS oncogene are present in 5-11% of head and neck squamous cell carcinomas (HNSCC), but whether mutant HRAS drives HNSCC growth was not known. The clinical candidate FTI, tipifarnib, is currently under investigation in HRAS-mutant HNSCC, but whether patient responses to tipifarnib are due to blocking HRAS membrane association or due to action on another FTI target/s is also unclear. We found that the FTIs tipifarnib and lonafarnib inhibited the growth of HRAS-mutant HNSCC in a target-dependent manner, blocking HRAS farnesylation and membrane association. We also found that genetic depletion of mutant HRAS inhibited the anchorage-dependent and -independent growth of HRAS-mutant HNSCC cell lines in vitro and robustly induced apoptosis, indicating HNSCC dependence on mutant HRAS and a correlation between FTI-mediated growth inhibition and blockade of HRAS function. Tumor types driven by other RAS isoforms, such as KRAS-driven pancreatic cancer, are highly dependent on the ERK MAPK effector pathway and are sensitive to pharmacological inhibitors of ERK1/2 (ERKi: SCH772984, BVD-523). In contrast, we found that HRAS-driven HNSCC was resistant to growth inhibition by ERKi alone, despite strong target inhibition as indicated by decreases in pRSK and MYC protein levels. Consistent with this finding, genetic depletion of HRAS not only failed to reduce MAPK signaling but instead caused compensatory upregulation. Similarly, FTI treatment also induced upregulation of MAPK signaling, which is typically growth-promoting. We therefore speculated that the addition of ERKi would enhance responses to FTIs, and indeed found that ERKi synergistically enhanced FTI-mediated apoptosis and growth inhibition. Our results provide a mechanistic rationale for adding ERKi to FTI to improve clinical responses in HRAS-mutant HNSCC, and suggest that monitoring MAPK pathway activation may be a useful marker for emerging FTI resistance in this patient population.

Citation Format: Sehrish Javaid, Victoria V. Nguyen, Andrew M. Waters, Craig M. Goodwin, Channing J. Der, Adrienne D. Cox. Farnesyltransferase inhibitor (FTI)-induced growth inhibition of HRAS-mutant head and neck cancers is enhanced by concurrently inhibiting compensatory upregulation of the ERK-MAPK kinase cascade [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-276.
Abstract LB-284: miRNAs/Ago2/YY1/PcG protein/DNMT complex mediates epigenetic silencing in bortezomib-induced apoptosis of leukemia
Authors: Wang Ju-Ming
Published: August 2019

miRNAs are a class of non-coding RNAs, which bind to the 3'-untranslated regions of their target mRNAs to repress translation. However, the details of miRNA-mediated epigenetic regulation targeting genomic DNA remained largely unknown. Here, we demonstrated that transcription factor CCAAT/enhancer binding protein delta (CEBPD) was responsive to the anticancer drug bortezomib, is a highly selective reversible inhibitor for leukemia treatment, and resulting in caspase activation and apoptosis. Interestingly, following the identification of CEBPD-induced miRNAs, we found that miR-744, miR-3154 and miR-3162 feedback to suppress the transcription of CEBPD itself and genes adjacent to its 5'-flanking region, including protein kinase DNA-activated catalytic polypeptide (PRKDC), minichromosome maintenance-deficient 4 (MCM4) and ubiquitin-conjugating enzyme E2 variant 2 (UBE2V2), upon bortezomib treatment. Additionally, we previously demonstrated that the Yin Yang 1 (YY1)/polycomb group (PcG) protein/DNA methyltransferase (DNMT) complex is important for mediating epigenetic silencing of the CEBPD gene; we further found that Argonaute 2 (Ago2) interacts with YY1 and binds to the CEBPD promoter. Moreover, we revealed that miRNA binding plays a key role for YY1/PcG group protein/DNMT complex-mediated epigenetic gene silencing and is associated with bortezomib-induced methylation on genomic DNA. Altogether, we provided new insights for miRNA-mediated epigenetic regulation in the case of bortezomib-induced cell death in leukemia.

Citation Format: Ju-Ming Wang. miRNAs/Ago2/YY1/PcG protein/DNMT complex mediates epigenetic silencing in bortezomib-induced apoptosis of leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-284.
Abstract LB-295: Therapeutic implications of altered cholesterol homeostasis mediated by loss of CYP46A1 in human glioblastoma
Authors: Han Mingzhi , Wang Shuai , Li Xingang , Wang Jian , Bjerkvig Rolf
Published: August 2019

BACKGROUND

Tumor cells display higher cholesterol levels compared to normal cells and emerging evidence indicates a pivotal role of cholesterol content in tumor cell proliferation and growth mediated by a dysregulation of key regulators involved in cholesterol homeostasis has been implicated in various cancers. In this study, we assessed the dependency of glioblastoma (GBM) cells to extracellular cholesterol levels for growth. Through analysis of whole-transcriptome databases, we identified the cholesterol homeostasis-related genes whose expression are dysregulated in gliomas. One of the most dramatically down-regulated genes identified encodes cholesterol 24-hydroxylase (CYP46A1), a brain-specific enzyme responsible for elimination of cholesterol via conversion of cholesterol to 24(S)-hydroxycholesterol (24OHC).

METHODS

Molecular and clinical data was obtained from publicly genomic databases. Immunohistochemistry was applied to assess the protein level of CYP46A1 in tissue microarrays. Functionally, CYP46A1 overexpression was determined using lentiviral constructs in LN229 and a primary glioblastoma cell line (GBM#P3). Cells were characterized in vitro and implanted in vivo to generate orthotopic xenografts in order to assess their molecular status, cell survival, and self-renewal by western blotting, flow cytometry, and extreme limiting dilution assay (ELDA), respectively.

RESULTS

Down-regulation of CYP46A1 was found in malignant glioma samples compared to normal brain tissue. Importantly, reduced CYP46A1 expression was associated with aggressive clinicopathological features and poor prognosis of GBM patients. In functional assays, restoration of CYP46A1 suppressed cell proliferation and in vivo tumour growth by increasing 24OHC levels. Consistent, treatment of GBM cells with 24OHC inhibited tumour growth and induced apoptosis in a concentration dependent manner. RNA-seq data showed that 24OHC regulated LXR and sterol regulatory-element binding protein 1 (SREBP1) signalling activity.

Intriguingly, efavirenz (EFV), a widespread used anti-HIV medication that effectively penetrates the blood–brain barrier, has recently been reported as a potent activator of the CYP46A1 enzyme. The therapeutic potential of EFV is currently being assessed in vivo and the data will be presented.

CONCLUSIONS

Collectively, our findings demonstrate that CYP46A1 is a critical cellular cholesterol regulator in GBM and that the CYP46A1/24OHC axis is a potential therapeutic target in GBM.

Citation Format: Mingzhi Han, Shuai Wang, Xingang Li, Jian Wang, Rolf Bjerkvig. Therapeutic implications of altered cholesterol homeostasis mediated by loss of CYP46A1 in human glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-295.
Abstract LB-299: A comprehensive platform of patient-derived xenografts and matched cell lines mirrors the genomic landscape of colorectal cancer
Authors: Lazzari Luca , Corti Giorgio , Isella Claudio , Montone Monica , Arcella Pamela , Zanella Eugenia , Novara Luca , Barbosa Fabiane , Cassingena Andrea , Cancelliere Carlotta , Medico Enzo , Sartore-Bianchi Andrea , Siena Salvatore , Bertotti Andrea , Trusolino Livio , Nicolantonio Federica Di , Linnebacher Michael , Bardelli Alberto , Arena Sabrina
Published: August 2019

Preclinical models that accurately reflect patients’ tumor with regards to histopathology, genomics, and therapeutic response represent a compelling need to fuel the progress of effective cancer treatments. Patient-derived tumor xenografts (PDXs) have significantly accelerated this process, but, although they closely mirror structural and molecular features of the tumor of origin, they still retain important restrictions related to maintenance costs and large-scale screening. To overcome this issue, we have established a novel platform of 2D-cell lines (xeno-cell lines, XL) derived from PDXs of colorectal cancer (CRC) from which patient’s germline gDNA was available. We have characterized XL-cells at multiple levels to confirm their proximity to the PDXs of origin and to assess their suitability as patient avatars in vitro to interrogate functional networks in colorectal cancer. All XL-cells showed an epithelial-like morphology and phenotype, as also confirmed by EMT biomarker transcriptomic analysis. Whole exome and RNA-seq analyses showed that genomic features were consistently preserved between PDXs and matched cell models. Expression analysis revealed the XL-line collection as a significant representative of all CRC subtypes (CMS and CRIS subgroups). Furthermore, genomic analysis allowed the identification of molecular biomarkers of response and resistance to targeted therapies, including EGFR and HER2 blockade. In particular, molecular determinants of resistance to dual-HER2 blockade previously reported in the Heracles-A trial were validated in XL-cells. In conclusion, the XL-cell line and PDX platform represents a unique and comprehensive preclinical tool to validate gene function e to identify novel pharmacological vulnerabilities in colorectal cancer.

Citation Format: Luca Lazzari, Giorgio Corti, Claudio Isella, Monica Montone, Pamela Arcella, Eugenia Zanella, Luca Novara, Fabiane Barbosa, Andrea Cassingena, Carlotta Cancelliere, Enzo Medico, Andrea Sartore-Bianchi, Salvatore Siena, Andrea Bertotti, Livio Trusolino, Federica Di Nicolantonio, Michael Linnebacher, Alberto Bardelli, Sabrina Arena. A comprehensive platform of patient-derived xenografts and matched cell lines mirrors the genomic landscape of colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-299.
Abstract SY15-03: Coding and noncoding genome for blood biopsy
Authors: Hayes Daniel F. , Alix-Panabières Catherine , Calin George A.
Published: August 2019

The development of effective diagnostic and prognostic biomarkers is crucial for early detection of cancer, prediction of clinical outcome, detection and monitoring minimal residual disease, and identification of patients who can benefit from therapy. Furthermore, they can provide important information of biological characteristics of tumor. Liquid biopsy, an alternative and non-invasive technique to surgical biopsy, enables the investigation of tumor markers in biological fluids, such as serum/plasma, urine, saliva, and pleural effusion. Increasing interest on liquid biopsy has grown over the past decade with particular focus on circulating non-coding RNAs (ncRNAs) and tumor-derived cell-free DNA (cfDNA) as cancer biomarkers. Owing to their high abundance and stability in biological fluids, circulating ncRNAs and tumor-derived cell-free DNA have potential utility to provide information on tumor biology (e.g.: EGFR and PIK3CA mutational status) which can help both diagnosis and prediction of effects of treatments, including standard treatment, targeted therapies, and immunotherapies. Recent advances in the field have highlighted the role of circulating ncRNAs in cell-to-cell communication. Particularly, ncRNAs can be transported through extracellular vesicle-mediated transfer to recipient cells, where they exert their functions of gene expression regulation, with implications for cancer progression and therapy resistance. This characteristic of circulating ncRNAs introduces an additional step in the information on tumor biology that can be obtained from liquid biopsy. Besides cancer, ncRNAs can also serve as biomarkers for microbial infection. Indeed, miRNAs originated from non-human genomes (xeno-miRNAs), such as viral miRNAs (Epstein-Barr virus, Kaposi sarcoma-associated herpesvirus), have been shown to be present in human body fluids. They can be used as biomarkers for diagnosis, prediction of clinical outcome, and the can also mediate cell-to-cell communication. Liquid biopsy has the potential to serve as additional tool to improve diagnosis, prognosis, prediction of treatment responses, and can provide information of biological characteristics of tumor.

Citation Format: Daniel F. Hayes, Catherine Alix-Panabières, George A. Calin. Coding and noncoding genome for blood biopsy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr SY15-03.
Abstract SY19-02: Metabolic tumor suppressors and disease progression
Authors: Simon M Celeste
Published: August 2019

Altered tumor cell metabolism is now firmly established as a hallmark of human cancer. Downstream of oncogenic events, metabolism is re-wired to support cellular energetics and supply the building blocks for biomass expansion and cell motility. Rapid, uncontrolled proliferation results in tumor growth beyond the reach of existing vasculature and triggers cellular adaptations to overcome limiting nutrient and oxygen delivery. However, oncogenic activation and metabolic re-programming also elicit cell intrinsic stresses, independent of the tumor microenvironment. To ensure metabolic robustness and stress resistance, pro-growth signals downstream of oncogene activation or tumor suppressor loss simultaneously activate homeostatic processes. Here, I will summarize adaptive mechanisms based on loss of fructose-1,6-bisphosphatases FBP1 and FBP2 in the settings of renal carcinoma, liver cancer, and soft tissue sarcoma. Both FBPs function in the cytoplasm and the nucleus to carry out enzymatic activity-dependent and -independent processes that suppress tumor growth. FBP1 and FBP2 impact both malignant and stromal cells in the tumor microenvironment, including inflammayory cells. Ultimately, an understanding of the adaptations required downstream of specific metabolic tumor suppressors could reveal targetable metabolic vulnerabilities.

Citation Format: M Celeste Simon. Metabolic tumor suppressors and disease progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr SY19-02.
Abstract SY21-02: Oncometabolites suppress homologous recombination DNA repair by inhibition of chromatin remodeling at the DNA double-strand break
Authors: Sulkowski Parker S. , Oeck Sebstian , Li Jing , Shuch Brian , King Megan C. , Bindra Ranjit S. , Glazer Peter M.
Published: August 2019

Elevated levels of the metabolites, 2-hydroxyglutarate (2HG), fumarate, and succinate, can occur in human malignancies due to somatic mutations in the isocitrate dehydrogenase 1/2 (IDH1/2) genes or germline mutations in fumarate hydratase (FH) and succinate dehydrogenase (SDH) genes, respectively. Mutations in IDH1 and IDH2 are found in a large number of human malignancies, most notably gliomas and acute myelogenous leukemias, along with cholangiocarcinomas, chondrosarcomas, and melanomas. Inherited mutations in FH and SDH, are linked to the familial cancer predisposition syndromes, Hereditary Leiomyomatosis and Renal Cell Cancer (HLRCC) and Hereditary Paraganglioma and Pheochromocytoma (SDH PGL/PCC), respectively. These structurally related metabolites inhibit α-ketoglutarate-dependent enzymes, including dioxygenases that modify chromatin. We have shown that they consequently suppress the pathway of homology-dependent DNA repair (HDR), conferring an exquisite sensitivity to PARP inhibitors that is currently being tested in clinical trials. In this presentation, we will discuss our recent work elucidating the mechanistic basis for this suppression of DNA repair. Rather than acting indirectly through epigenetic regulation of gene expression, we find that these metabolites act directly by inhibiting HDR factor recruitment to DNA double-strand breaks (DSBs). The metabolites inhibit the lysine demethylases, KDM4A/B, causing aberrant hypermethylation of H3K9 and disrupting signaling at the break, thereby delaying the stepwise recruitment of key HDR factors. These results define a novel mechanism of decreased DNA repair in oncometabolite producing human tumors and may provide the basis for the rational design of novel therapeutic strategies for these malignancies.

Citation Format: Parker S. Sulkowski, Sebstian Oeck, Jing Li, Brian Shuch, Megan C. King, Ranjit S. Bindra, Peter M. Glazer. Oncometabolites suppress homologous recombination DNA repair by inhibition of chromatin remodeling at the DNA double-strand break [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr SY21-02.
Abstract SY25-02: Widespread germline-somatic regulatory differences in renal cell carcinoma prioritize risk mechanisms
Authors: Gusev Alexander , Spisak Sandor , Abbasi Forough , Fay Andre , Carol Hallie , Seo Ji-Heui , Choueiri Toni , Lawrenson Kate , Freedman Matthew
Published: August 2019

Determining the function of non-coding regulatory variants in cancer remains a key challenge. We investigated genetic (germline and somatic) determinants of regulatory mechanisms in renal cell carcinoma (RCC) using H3K27ac ChIP-seq data in 10 matched tumor/normal samples and RNA-seq data from 496/66 tumor/normal samples from The Cancer Genome Atlas (TCGA). Unsupervised clustering of H3K27ac activity cleanly separated tumor from normal individuals, highlighting extensive epigenetic reprogramming during transformation. We developed a novel method to test each chromatin feature for allele-specific activity (asQTL) and evaluate tumor/normal differences in allele-specificity (d-asQTLs) while modelling local structural variation and read overdispersion. At an FDR of 5%, we identified 1,356 unique asQTL chromatin peaks in normal tissues; 2,868 in tumors; and 1,054 d-asQTLs (primarily imbalanced in tumor). The d-asQTL peaks were significantly enriched for RCC GWAS heritability (32x, P=1.8x10-3), more so than any other functional feature including all H3K27ac peaks (12x), super-enhancers (5x), and regions near asQTL genes (4x). Intersection of asQTLs with RCC genome-wide association study (GWAS) data identified putative functional features for 6/17 known loci including tumor-specific activity at SCARB1, which has recently been implicated as a prognostic biomarker in RCC. d-asQTLs were significantly enriched for tumor-specific binding of transcription factors in the hypoxia pathway, implicating a general mechanism for polygenic germline-somatic interaction.

Citation Format: Alexander Gusev, Sandor Spisak, Forough Abbasi, Andre Fay, Hallie Carol, Ji-Heui Seo, Toni Choueiri, Kate Lawrenson, Matthew Freedman. Widespread germline-somatic regulatory differences in renal cell carcinoma prioritize risk mechanisms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr SY25-02.
Abstract SY31-01: Development and validation of a clinical-grade cell-free DNA profiling assay: MSK-ACCESS
Authors: Tsui Dana Wai Yi
Published: August 2019

Cell-free DNA profiling noninvasively reveals the underlying tumor genomic profiles to guide treatment decisions, especially important when the tumor is in a site that is difficult or risky to access. It has the potential to guide treatment stratification, monitor disease responses, identify resistance mechanisms and detection of minimal residual disease or relapse.Clinical implementation of molecular profiling assay requires the establishment of robust quality controls throughout the process including pre-analytical procedures, such as sample collection and processing, analytical steps such as molecular assay specification and bioinformatics algorithm, as well as data reporting.

This talk will describe an academic institutional effort to develop and validate a clinical-grade cell-free DNA profiling assay for patient care. We will discuss considerations behind the development, including factors such as analytical sensitivity required for individual clinical applications, operational and logistical efficiency, regulatory requirement and clinical annotation to guide decisions. We will also present the validation studies required by the New York State Department of Health to demonstrate robustness of the assay before clinical deployment.

The assay we have developed, called MSK-ACCESS (Analysis of Circulating cfDNA to Evaluate Somatic Status), is a custom next-generation sequencing assay covering selected exons from 129 cancer-related genes for ultra-sensitivity detection of somatic mutations from plasma. Using ultra-high depth (>15,000x) sequencing, with duplex unique molecular indexing (UMI), unique dual sample barcodes, and background error suppression, MSK-ACCESS is able to detect low-frequency (0.1%) variants with high confidence. We validated MSK-ACCESS using plasma samples collected from healthy non-cancer individuals and cancer patients with known mutations in selected genes of interest. We evaluated the analytical performance of the assays such as accuracy, intra- and inter-assay reproducibility using control samples and samples with known mutation data established by orthogonal assays. With the growing interest on cell-free DNA profiling for molecular diagnostics, it is crucial to ensure robustness of each assay to deliver high-quality data to guide decisions. Establishing analytical performance is the first step precedes large-scale prospective trials to further demonstrate clinical utility of cell-free DNA as a biomarker.

Citation Format: Dana Wai Yi Tsui. Development and validation of a clinical-grade cell-free DNA profiling assay: MSK-ACCESS [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr SY31-01.
Abstract SY37-03: Clock-HIF signaling in the epigenetic control of glucose metabolism
Authors: Peek Clara Bien
Published: August 2019

Circadian systems play a central role in energy harvesting and storage across daily cycles of fuel availability. In vertebrates, clock genes promote metabolic constancy by coordinating the phase and expression of genes involved in glycolytic and oxidative metabolism. Our previous studies, as well as those from others, revealed that circadian transcription factors (TFs) display functional interactions with the hypoxia-inducible factor (HIF) pathway. Our previous studies demonstrated impaired hypoxic expression of known canonical HIF target genes in Bmal1-/- myotubes and fibroblasts, including those involved in anaerobic glycolysis, angiogenesis, and the HIF pathway. We also observed time-of-day-dependent activation of HIF targets in muscle tissue, raising the possibility that the clock acts to ‘gate’ the induction of HIF targets at different circadian phases. Moreover, we found that hypoxia and HIF can reciprocally regulate direct BMAL1 targets, suggesting a close association between hypoxic and circadian transcriptional networks. Finally, transcriptome profiling studies reveal strikingly little overlap in the subset of BMAL1-dependent genes in normoxia versus hypoxia, suggesting either global remodeling of ‘accessible’ chromatin at sites of promoters and enhancers allowing for altered BMAL1-dependent transcription. Collectively, our data reveal coupling of the HIF and circadian TF pathways producing rhythmic adaptation to hypoxic stress.

Citation Format: Clara Bien Peek. Clock-HIF signaling in the epigenetic control of glucose metabolism [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr SY37-03.
Abstract SY42-03: Systematic interrogation of cancer dependencies and synthetic lethal interactions
Authors: Hahn William C.
Published: August 2019

Although molecular profiling of human tumors is becoming increasingly routine, the use of this data to guide remains limited to a subset of patients. To complement genome characterization studies, we have used genome scale gain and loss of function approaches to identify genes required for cell survival and transformation. Specifically, we have performed systematic studies to interrogate rare alleles found altered in cancer genomes and used advances in synthetic gene synthesis to prospectively interrogate all possible alleles of known cancer genes. In parallel, we have performed both genome scale RNAi and CRISRP-Cas9 screens in hundreds of cancer cell lines to identify differentially essential genes and the context that specifies gene dependency. Integrating these studies with genome characterization of human tumors and protein-protein interaction databases facilitates the identification of genes and pathways required for the survival of specific cancer subtypes. These studies allow us to define a global cancer dependencies map, which will help further operationalize precision cancer medicine.

Citation Format: William C. Hahn. Systematic interrogation of cancer dependencies and synthetic lethal interactions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr SY42-03.