bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3512: Ikaros regulation of the BCL6/BACH2 axis and its clinical relevance in acute lymphoblastic leukemia
Authors: Song Chunhua , Ge Zheng , Li Jianyong , Chen Baoan , Dovat Elanora , Dovat Katarina , Payne Jonathon , Dovat Sinisa
Published: July 2017

B-Cell CLL/Lymphoma 6 (BCL6) is a proto-oncogene that is highly expressed in acute lymphoblastic leukemia (ALL). BTB and CNC Homology 1 Basic Leucine Zipper Transcription Factor 2 (BACH2) is a suppressor of transcription. The BACH2-BCL6 balance controls selection at the pre-B cell receptor checkpoint by regulating p53 expression. However, the underlying mechanism and the clinical relevance of the BCL6/BACH2 axis are unknown. Here, we found that Ikaros, a tumor suppressor encoded by IKZF1, directly binds to both the BCL6 and BACH2 promoters where it suppresses BCL6 and promotes BACH2 expression in B-cell ALL (B-ALL) cells. Casein kinase 2 (CK2) inhibitors increase Ikaros function thereby inhibiting BCL6 and promoting BACH2 expression in an Ikaros-dependent manner. We also found that the expression of BCL6 is higher while BACH2 expression is lower in patients with B-ALL than normal bone marrow control. High BCL6 and low BACH2 expression is associated with high leukemic cell proliferation, unfavorable clinical and laboratory features, and inferior outcomes. Moreover, IKZF1 deletion is associated with high BCL6 and low BACH2 expression in B-ALL patients. CK2 inhibitors increase Ikaros binding to the promoter of BCL6 and BACH2 and suppress BCL6 while promoting BACH2 expression in the primary B-ALL cells. Our data indicates that Ikaros regulates expression of the BCL6/BACH2 axis in B-ALL. High BCL6 and low BACH2 expression are associated with Ikaros dysregulation and have a potential effect on the development of B-ALL.

Citation Format: Chunhua Song, Zheng Ge, Jianyong Li, Baoan Chen, Elanora Dovat, Katarina Dovat, Jonathon Payne, Sinisa Dovat. Ikaros regulation of the BCL6/BACH2 axis and its clinical relevance in 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 3512. doi:10.1158/1538-7445.AM2017-3512
Abstract 3516: RUNX1 controls EGFR signaling pathway in non-small cell lung cancer cells
Authors: Matsuo Akihiko
Published: July 2017

Epidermal growth factor receptor (EGFR) is a promising target for anticancer therapy for non-small lung cancer (NSCLC). Mitogen-inducible gene 6 (Mig6) is known to be a negative feedback regulator of EGFR. Mig6 inhibits EGFR kinase activity and promote wild-type EGFR trafficking to the degradation pathway. Down-regulation of Mig6 is found in poor prognostic NSCLC. Previous gene array analysis results suggested that Mig6 is downregulated by runt-related transcription factor 1 (RUNX1), yet the detailed relationship between RUNX1 and Mig6 in NSCLC has not been elucidated. Herein we demonstrate that RUNX1 inhibition is effective for wild-type EGFR NSCLC. Tet-inducible shRNA mediated RUNX1 knockdown in wild-type EGFR cell line LU99A led to the increased expression of Mig6 and decreased expression of phosphorylated form of EGFR as well as deactivation of EGFR/ERK pathway. RUNX1 knockdown subsequently induced apoptosis in LU99A cells. Silencing of Mig6 in LU99A cells promoted the proliferation of these cancer cells and increased expression of phosphorylated form of EGFR, highlighting the importance of this EGFR signaling cascade in the maintenance of wild-type EGFR NSCLC. Indeed, RUNX1 overexpression promoted cell proliferation and decreased expression of Mig6 and increased phosphorylated form of EGFR. Notably Mig6 knockdown in RUNX1 knockdown LU99A cells increased their proliferation rates, indicating that Mig6 plays an important role in RUNX1-mediated pro-oncogenic pathway. We next examined the efficacy of a novel small molecule which specifically binds and inhibits the RUNX1 (We named it as CM). CM was drastically effective for wild-type EGFR NSCLC cell lines A549 and LU99A which are naturally resistant to EGFR Tyrosine kinase inhibitor: gefitinib. In addition, CM suppressed tumor growth of xeno-transplanted A549 cells in immune-deficient mice in vivo. Our study underscores the importance of RUNX1 inhibition therapy in the management of gefitinib-resistant NSCLC patients.

Citation Format: Akihiko Matsuo. RUNX1 controls EGFR signaling pathway in non-small cell lung 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 3516. doi:10.1158/1538-7445.AM2017-3516
Abstract 3523: Arginyltransferase1 as a novel suppressor of prostate cancer metastasis
Authors: Birnbaum Michael , Kumar Akhilesh , Morgan William , Zhang Fangliang
Published: July 2017

Arginylation is a post-translational modification wholly mediated by Arginyltransferase 1 (Ate1). Our studies have shown that Ate1 and arginylation are upregulated during stress conditions. In addition, it was recently shown that Ate1-deficient fibroblasts demonstrate cancer-like characteristics including genomic instability and mutagenesis. While Ate1’s role in cancer is poorly understood, our preliminary studies suggest that Ate1 is an important regulator of metastasis and cancer progression in prostate cancer models. In this study, our data suggests that Ate1 is essential for normal cell stress response in conditions including cellular oxidant, apoptosis inducing drugs, and radiation. Further, we show that a loss of Ate1 in LnCaP prostate cancer cells increases anchorage-independent growth in the soft-agar assay, and that a loss of Ate1 in PC-3 prostate cancer cells increases matrigel invasion in the Boyden chamber assay. To text how Ate1 affects metastasis in vivo, PC-3 cells with Ate1 or control shRNA were orthotopically implanted into the prostates of immunocompromised mice to observe metastasis. While very little metastasis was observed in PC-3 control cells, PC-3 cells with reduced Ate1 achieved much higher levels of metastasis. In conclusion, our data suggests that the loss of Ate1 in prostate cancer promotes cancer progression phenotypes and cell survival. In future studies, we will examine if Ate1 levels in human prostate cancers in prostate cancer prognosis.

Citation Format: Michael Birnbaum, Akhilesh Kumar, William Morgan, Fangliang Zhang. Arginyltransferase1 as a novel suppressor of prostate cancer metastasis [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 3523. doi:10.1158/1538-7445.AM2017-3523
Abstract 3527: Clarification of the molecular mechanism for cancer development in Xp11.2 translocation renal cell carcinoma
Authors: Baba Masaya , Huang Ying , Motoshima Takanobu , Hasumi Hisashi , Hasumi Yukiko , Furuya Mitsuko , Nagashima Yoji , Yao Masahiro , Oike Yuichi , Kamba Tomomi , Schmidt Laura S. , Linehan W. Marston
Published: July 2017

Xp11.2 translocation renal cell carcinoma (Xp11.2 tRCC) is a newly defined subset of RCC, which have chromosomal translocations involving the TFE3 transcription factor at Xp11.2. All translocations seen in Xp11.2 tRCC, including PRCC-TFE3, PSF-TFE3, ASPL-TFE3, CTLC-TFE3 and NONO-TFE3 produce chimeric TFE3 genes, which encode fusion TFE3 proteins retaining the basic helix-loop-helix leucine zipper (bHLH-Zip) structure for DNA binding, suggesting that these fusion TFE3 proteins function as oncogenic transcription factors. To clarify the molecular mechanism for Xp11.2 tRCC development, we have established cell lines, which express fusion TFE3 proteins (NONO-TFE3, PRCC-TFE3, PSF-TFE3) in a doxycycline dependent manner. Genes upregulated universally in all fusion TFE3 cell lines upon doxycycline addition were identified. In addition, we have generated an Xp11.2 translocation RCC mouse model, in which a floxed Neomycin cassette followed by a PRCC-TFE3 cDNA is inserted in the Rosa26 locus. By crossing these mice with cadherin 16-Cre transgenic mice, we can induce kidney specific PRCC-TFE3 expression resulting in RCC development. We will report and discuss the role of fusion TFE3 target genes in our mouse model and in clinical samples of Xp11.2 tRCC. Funded in part by FNLCR Contract HHSN261200800001E to LSS.

Citation Format: Masaya Baba, Ying Huang, Takanobu Motoshima, Hisashi Hasumi, Yukiko Hasumi, Mitsuko Furuya, Yoji Nagashima, Masahiro Yao, Yuichi Oike, Tomomi Kamba, Laura S. Schmidt, W. Marston Linehan. Clarification of the molecular mechanism for cancer development in Xp11.2 translocation renal cell carcinoma [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 3527. doi:10.1158/1538-7445.AM2017-3527
Abstract 3529: Investigating the in vivo role of the EHF transcription factor in intestinal epithelial differentiation
Authors: Reehorst Camilla M. , Luk Ian Y. , Nightingale Rebecca , Davalos-Salas Mercedes , Dhillon Amardeep S. , Mariadason John M.
Published: July 2017

Objective: Poor tumor differentiation status is associated with worse patient outcome in colorectal cancer. However, the molecular basis for loss of differentiation in colon cancer is not well understood. We have found that the transcription factor Ets homologous factor (EHF) is highly expressed in the normal human and mouse colonic epithelium and is down-regulated in poorly-differentiated colorectal cancer cell lines. The aim of this study was to investigate the role of EHF in regulating normal colonic epithelial cell differentiation in vivo.

Methods: A novel mouse model was generated in which the Ets DNA binding domain (exon 8) of EHF was flanked by loxP sites (EHFlox/lox). To inactive EHF in the intestinal epithelium, EHFlox/lox mice were crossed to Villin-CreERT2 mice and recombination induced by tamoxifen treatment. Tamoxifen and vehicle treated mice were monitored weekly for up to one year. At each endpoint, tissue was collected and the effect of EHF deletion on intestinal cell proliferation and differentiation assessed by qRT-PCR and immunohistochemistry.

Results: Targeted inactivation of EHF in the small intestinal and colonic epithelium following tamoxifen treatment was confirmed at the DNA and RNA level. EHF inactivation in the intestinal epithelium had minimal effect on survival, weight gain and overall health of the animals. Furthermore, loss of EHF did not markedly affect cell proliferation or the overall architecture of the intestinal epithelium. Finally, EHF inactivation also had minimal effect on markers of absorptive, enteroendocrine or Paneth cell differentiation but did reduce the number of goblet cells in the colonic epithelium.

Conclusion: EHF does not play a major role in regulating cell proliferation in the mouse intestine but may play a role in regulating goblet cell differentiation. The role of EHF in intestinal tumourigenesis and response to stress are currently being investigated.

Citation Format: Camilla M. Reehorst, Ian Y. Luk, Rebecca Nightingale, Mercedes Davalos-Salas, Amardeep S. Dhillon, John M. Mariadason. Investigating the in vivo role of the EHF transcription factor in intestinal epithelial differentiation [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 3529. doi:10.1158/1538-7445.AM2017-3529
Abstract 3533: Connections between NF-κB misregulation and carcinogenesis
Authors: Chyong Donian I. , Naderi Aurian , Lee Chase , Arpornsuksant Ty , Lu Allison , Dilip Megha , Zhang Margaret , Surh Young-Joon , Lee Eun-Ji , Na Hye-Kyung
Published: July 2017

In this review poster, we researched the function, regulation, and structure of NF-κB as it relates to carcinogenesis. Found in almost all animal cells, nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) is a transcription factor that plays various roles in cellular proliferation, cell survival, inflammation, and T cell activation. There are two different NF-κB signaling pathways: the canonical pathway and the non-canonical pathway. NF-κB forms a p50/Rel A heterodimer in the canonical pathway and a p52/ Rel B heterodimer in the non-canonical pathway. NF-κB protein is normally sequestered in the cytoplasm as an inactive complex with a κB inhibitor (IκB) protein. Outside stimuli such as reactive oxygen species (ROS) and tumor necrosis factor alpha (TNF-α) activate cell surface receptors such as Toll-Like Receptors (TLRs) and Receptor Activators of NF-κB (RANK). These surface receptors, in turn, activate IκB kinase (IKK). IKK phosphorylates IκB, which causes ubiquitination of IκB, signaling proteasomes to degrade it. NF-κB then enters the nucleus through a nuclear pore and forms a transcription complex with coactivators and RNA polymerase. NF-κB binds to specific DNA-binding sites to induce transcription. One of the target genes of NF-κB encodes IκBs, so NF-κB regulates its own activity through a negative feedback loop. Because the cell maintains storage of the signaling protein NF-κB in the cytoplasm, NF-κB allows the cell to respond to sudden stimuli by activating quick changes in gene expression. Because proteins that promote cellular proliferation and cell survival are mainly transcribed through NF-κB activation, uncontrolled overactivation of this transcription factor has major implications in carcinogenesis. Many types of cancer cells have high levels of constitutively active NF-κB. Mutations in the genes for NF-κB itself or its inhibitors such as IκBs often found in cancer cells can cause cells to accelerate their proliferation or confer resistance to apoptosis. Some types of cancer cells secrete signaling molecules, inducing improper NF-κB activity. Because of the tumor promoting characteristics of NF-κB activation, a focus of current research is to find methods of suppressing NF-κB to kill cancer cells or slow their growth. We designed a 3D-printed model of the p50/RelA NF-κB protein using Jmol to highlight the relationship between its structure and function.

Citation Format: Donian I. Chyong, Aurian Naderi, Chase Lee, Ty Arpornsuksant, Allison Lu, Megha Dilip, Margaret Zhang, Young-Joon Surh, Eun-Ji Lee, Hye-Kyung Na. Connections between NF-κB misregulation and carcinogenesis [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 3533. doi:10.1158/1538-7445.AM2017-3533
Abstract 3535: Methylation regulates HEY1 expression in glioblastoma
Authors: Guda Maheedhara Reddy , Tsung Andrew J. , Asuthkar Swapna , Labak Collin M. , Lu Yining , Martin Sarah E. , Durbaka Prasad V. , Velpula Kiran K.
Published: July 2017

Glioblastoma multiforme (GBM) remains one of the most lethal and difficult-to-treat cancers of the central nervous system despite the existence of multi-modal therapeutic approaches. The poor prognosis in GBM patients is due in part to its resistance to available treatments, which calls for identifying novel molecular therapeutic targets. In this study, we identified an interesting biomarker, Hairy/Enhancer-Of-Split related with YRPW Motif (HEY1), a mediator of Notch signaling, which contributes to the pathogenesis of GBM. Datamining studies and our immunohistochemistry and immunoblot analysis showed that HEY1 is highly expressed in GBM patient specimens. Recent studies indicate that methylation status may control the expression of cancer phenotype. Our studies using bisulphite sequencing on the patient samples showed that HEY1 promoter was hypermethylated in the normal brain when compared to GBM specimens. Treatment on the 4910 and 5310 xenograft cell lines with sodium butyrate (NaB) greatly decreased HEY1 expression owing to its promoter hypermethylation with a concomitant increase in DNMT1 expression confirming that promoter methylation regulate the HEY1 expression in GBM. NaB treatment also induced cell apoptosis as evaluated by flow cytometric analysis. Silencing HEY1 reduced invasion, migration and proliferation in 4910 and 5310 cells. Further, immunoblot and q-PCR analysis demonstrated the existence of a potential positive regulatory loop between HEY1 and p53. Additionally, DNA microarrays with HEY1 recombinant protein demonstrated good correlation with p53 and provided various bonafide targets of HEY1. Collectively, these studies suggest HEY1 as an important predictive marker for GBM, thus indicating a potential target for future GBM therapy.

Citation Format: Maheedhara Reddy Guda, Andrew J. Tsung, Swapna Asuthkar, Collin M. Labak, Yining Lu, Sarah E. Martin, Prasad V. Durbaka, Kiran K. Velpula. Methylation regulates HEY1 expression in glioblastoma [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 3535. doi:10.1158/1538-7445.AM2017-3535
Abstract 3546: LIN28B/MYC loop regulates aerobic glycolysis and tumor acidic microenvironment to promote cancer stemness and cancer progression
Authors: Chen Chong , Bai Lipeng , Cao Fengqi , wang shengnan , Liu Yan , Guo Jian , Si Qin , Xiang Rong , Luo Yunping
Published: July 2017

Substantial evidences have proven that targeting cancer addictive metabolism could suppress tumor progression. Tumor microenvironment (TME) supports the development of metabolic reprograming of tumor cells. The function of cancer stem cells (CSCs) closely related with its own metabolic alteration. However, the relationship between CSCs’ metabolic reprograming and their supportive TME, as well as underlying mechanism remains largely unknown. In this study, we have demonstrated a novel mechanism that the LIN28B/MYC positive regulation loop could promote the aerobic glycolysis of cancer cells and glycolysis-derived lactate and further enhance the cancer stemness to facilitate tumor progression. 1) Metabolic analysis revealed that glycolysis (ECAR) was suppressed after LIN28B was knocked down in MDA-MB-231 or H1299 cancer cells respectively. Consistently, both the glucose-uptake and lactate-secretion were attenuated in shLIN28B cancer cells. Importantly, either the glucose accumulation in cancer tissues or lactate secretion in serum was reduced in mouse injected with shLIN28B cancer cells. 2) Metabolic analysis revealed that CSCs possessed higher ECAR and higher level of LIN28B, MYC and HIF1a. Furthermore, glycolysis-derived lactate not only increase the proportion of ALDH+ cells, but also enhance the tumorsphere forming ability and mobility of cancer cells. 3) MicroRNAs screening analysis revealed that 6 miRNAs were up-regulated above 2 folds after LIN28B was knocked down in MDA-MB-231 cells. Metabolic analysis revealed that miR-34a-5p could suppress the aerobic glycolysis (ECAR) in MDA-MB-231 cells. 4) LIN28B inhibitor could reduce the expression of LIN28B and MYC in vitro and then suppressed tumor growth and metastasis in vivo. Taken together, our study demonstrated that LIN28B/MYC loop could sustain the aerobic glycolysis of cancer cells and then enhance the function of CSCs via regulating the tumor acid microenvironment, thus, established the LIN28B/MYC as a central node in connecting tumor metabolism and tumor microenvironment, and could serve as a therapeutical target.

Citation Format: Chong Chen, Lipeng Bai, Fengqi Cao, shengnan wang, Yan Liu, Jian Guo, Qin Si, Rong Xiang, Yunping Luo. LIN28B/MYC loop regulates aerobic glycolysis and tumor acidic microenvironment to promote cancer stemness and cancer progression [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 3546. doi:10.1158/1538-7445.AM2017-3546
Abstract 3558: Src regulation of peroxisome proliferator-activated receptor gamma (PPARγ) in lipid metabolism of lung cancer
Authors: Hua Tuyen N. M. , Phan Ai N. H. , Jeong Yangsik
Published: July 2017

Metabolic reprogramming, recently becoming one of the cancer hallmarks, is linked to oncogenic signal transduction to find a better solution for cancer therapy. As one of key mediators in oncogenic signal transduction, non-receptor tyrosine kinase Src is known to drive cancer progression by promoting cell proliferation, metastasis, and drug resistance. Although previous studies reported that Src promotes fat accumulation and suppresses browning of white adipocytes, little is known about the mechanistic role of Src in cancer metabolism. Here we report that Src mediates lipid mobilization by suppressing transcriptional activity of PPARγ, a key regulator of lipid metabolism. Firstly, we found Src suppression of PPARγ activity which, interestingly, turned out to be independent of Src kinase domain or a known Src phosphorylation site of PPARγ at tyrosine 78. Since the treatment of Src inhibitor (e.g., SU6656, PP2) could rescue Src-driven PPARγ suppression by possibly changing Src conformation, we might suggest the involvement of Src-PPARγ interaction in the regulatory mechanism. Mechanistically, further in vitro experiment showed Src inhibitor treatment recovered expression of PPARγ target genes such as fatty acid binding protein 4 (FABP4) and cluster of differentiation 36 (CD36) in a subset of non-small cell lung cancer cell lines. The increase of FABP4 and CD36 expression was associated with the reduction of lipid droplets, suggesting the role of Src regulation of PPARγ in lipid mobilization. Collectively, this finding provides better understandings about the role of Src in cancer lipid metabolism, and an insight into therapeutic combination of targeting oncogenic signal transduction and lipid metabolism to treat cancer.

Note: This abstract was not presented at the meeting.

Citation Format: Tuyen N. M. Hua, Ai N. H. Phan, Yangsik Jeong. Src regulation of peroxisome proliferator-activated receptor gamma (PPARγ) in lipid metabolism of lung 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 3558. doi:10.1158/1538-7445.AM2017-3558
Abstract 3562: A novel TGF-β signaling pathway promotes a slow growing phenotype of cancer cells in response to glutamine insufficiency
Authors: He Dan , Yin Chengqian , Qie Shuo , Chen Shuyang , Sang Nianli
Published: July 2017

Glutamine is a critical nutrient for proliferating cells and most tumor cells. Glutamine addiction as one of the dramatic tumor cell adaptive metabolisms is characterized by increased glutaminolysis. To better understand how tumor cells respond to glutamine deficiency, we cultured Hep3B cells in glutamine free media supplemented with ammonia, and isolated survival clones (MM01). These clones are capable of perpetual survival in glutamine free media with ammonia, but assume a slow growing phenotype, which represents the model adapted to long-term glutamine insufficiency. Comparing MM01 and Hep3B by microarray-based genome-wide gene expression profiling, we identified functional activation of Smad2/3 in MM01 cells, suggesting that long-term glutamine insufficiency activates a TGF-β signaling pathway. We have validated that glutamine insufficiency triggers Samd2 phosphorylation, which in turn, stimulates the expression of p15INK4B, providing a link to the slow growing phenotype. To elucidate how glutamine insufficiency triggers TGF-β signaling, we examined the effects of glutamine insufficiency on the expression levels of TGF-β family ligands, and found that Inhibin-βE, a newly discovered inhibin subunit isoform in the TGF-β superfamily, is up-regulated at both mRNA and protein levels in MM01. Luciferase assays demonstrate that glutamine insufficiency enhances the activity of Inhibin-βE promoter. Furthermore, we show that overexpressing Inhibin-βE is sufficient to induce Smad2/3 activation and growth inhibition in Hep3B cells. Taken together, our data suggest that Inhibin-βE likely plays a crucial role in cell adaptation to metabolic stress, facilitating cancer cell survival by slowing down biosynthesis and proliferation. A better understanding of the novel Inhibin-βE-triggered TGF-β signaling pathway may provide potential new therapeutic targets for cancer treatment.

Citation Format: Dan He, Chengqian Yin, Shuo Qie, Shuyang Chen, Nianli Sang. A novel TGF-β signaling pathway promotes a slow growing phenotype of cancer cells in response to glutamine insufficiency [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 3562. doi:10.1158/1538-7445.AM2017-3562
Abstract 3569: Comparative RNA-seq analysis reveals dys-regulation of major canonical pathways in ERG-inducible LNCaP cell progression model of prostate cancer
Authors: Kumar Parameet , Chakraborty Joyeeta , Chatterjee Raghunath , Sukumar Gauthaman , Dalgard Clifton L. , Babcock Kevin , Dobi Albert , Sreenath Taduru L. , Biswas Roopa
Published: July 2017

Prostate Cancer (CaP) is the most common non-cutaneous form of cancer in men and is the second leading cause of cancer mortality in men in the USA. In human CaP, gene fusion between androgen responsive regulatory elements at the 5' untranslated region of TMPRSS2 and ETS-related genes (ERG) is present in at least 50% of the prostate tumors. To identify and investigate the underlying mechanisms of ERG-associated CaP, we developed ERG-inducible LNCaP cell system. In this present study, we investigated the unique cellular transcriptome associated with over-expressed ERG in CaP cells. Our data from comprehensive transcriptome analyses, illustrate a distinct signature that distinguishes ERG-dependent and ERG-independent CaP. The data highlight the significant heterogeneity among the transcript. Out of the 527 differentially expressed genes, 232 genes were up-regulated and 295 genes were down-regulated in response to ERG. Subsequent, in silico analyses indicate that these differentially expressed genes were associated with many pathways and functions. The most significantly differentially expressed genes were associated with cell cycle regulation. The top-ranked biological functions affected by ERG over-expression include Cell Cycle (p < 1.42E-04), Cellular Growth and Proliferation (p < 1.23E-04), Cellular Development (p <1.23E-04), Cell Death and Survival (p < 1.37E-04), and Cellular Assembly and Organization (p < 1.42E-04). Further analyses indicate a strong association with known cancer networks. The top-ranked canonical pathways enriched in ERG-positive compared to ERG-negative LNCaP cells include, Cell Cycle Control of Chromosomal Replication (p=2.69E-16), Role of CHK Proteins in Cell Cycle Checkpoint Control (p=3.16E-11), Cell Cycle: G2/M DNA Damage Checkpoint Regulation (p=1.34E-09), Role of BRCA1 in DNA Damage Response (p=4.05E-08) and Estrogen-mediated S-phase Entry (p =5.51E-08). These findings indicate new insights into the complexity of TMPRESS2-ERG gene fusion, and may help understand mechanistic pathways which promote growth and progression of CaP.

Citation Format: Parameet Kumar, Joyeeta Chakraborty, Raghunath Chatterjee, Gauthaman Sukumar, Clifton L. Dalgard, Kevin Babcock, Albert Dobi, Taduru L. Sreenath, Roopa Biswas. Comparative RNA-seq analysis reveals dys-regulation of major canonical pathways in ERG-inducible LNCaP cell progression model of prostate 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 3569. doi:10.1158/1538-7445.AM2017-3569
Abstract 3570: Germline structural variant detection with variation graphs
Authors: Dawson Eric T. , Garrison Erik , Novak Adam , Paten Benedict , Eizinga Jordan , Hickey Glenn , Chanock Stephen , Durbin Richard
Published: July 2017

Structural variants play a major role in many cancers. However, classical methods of detection rely on searching for mapping signatures and a perpetual “rediscovering” of variants relative to the reference. A more efficient technique would be to map directly against known variants. We present a novel method for detecting known structural variants in next-generation sequencing data using variation graphs. Variation graphs are reference-like structures that succinctly encode the variation present within a population. Existing tools enable reads to be efficiently mapped against this graph structure. We are able to speed up queries for the presence or absence of variants by reducing the operation to a simple lookup in an external index. The current implementation of our variation graph approach is open source and publically available as part of the variation graph toolkit (https://github.com/vgteam/vg). Our method of variant typing on variation graphs has great potential to model and assess the complexity of cancer genomes while remaining efficient enough to make analysis tractable.

Citation Format: Eric T. Dawson, Erik Garrison, Adam Novak, Benedict Paten, Jordan Eizinga, Glenn Hickey, Stephen Chanock, Richard Durbin. Germline structural variant detection with variation graphs [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 3570. doi:10.1158/1538-7445.AM2017-3570
Abstract 3580: GATK CNV: copy-number variation discovery from coverage data
Authors: Babadi Mehrtash , Benjamin David I. , Lee Samuel K. , Smirnov Andrey , Chevalier Aaron , Lichtenstein Lee , Rubio Valentin Ruano
Published: July 2017

We propose and evaluate a novel algorithm for inferring germline and somatic copy number variation from whole exome sequencing (WES) and whole genome sequencing (WGS) data. Starting with the depth of aligned short reads from a cohort of samples, we use a Bayesian model for learning sequencing bias and simultaneously detecting CNV events using a hidden Markov model for change-point detection. A unified framework is used to call both germline and somatic CNVs. Denoising and event discovery are performed self-consistently to achieve maximum accuracy. In contrast to previous methods, our model naturally accounts for mixed sex cohorts and can detect events on sex chromosomes. Furthermore, we can detect excessively noisy samples and extract useful information within a probabilistic framework. Our implementation can also utilize Spark clusters, enabling the processing of larger cohorts and allowing for improved runtime performance.

We benchmark the new method for precision, recall, and reproducibility of both germline and somatic variants. Evaluations are performed on a cohort of WES samples from The Cancer Genome Atlas with matching WGS data. For germline variants, we use blood normal samples and compare our calls on WES data against Genome STRiP calls on WGS data. We find that GATK CNV yields remarkably higher precision and recall compared to XHMM and CODEX software packages. For somatic variants, we compare our calls against TITAN and find a remarkably high concordance.

Citation Format: Mehrtash Babadi, David I. Benjamin, Samuel K. Lee, Andrey Smirnov, Aaron Chevalier, Lee Lichtenstein, Valentin Ruano Rubio. GATK CNV: copy-number variation discovery from coverage 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 3580. doi:10.1158/1538-7445.AM2017-3580
Abstract 3581: GATK ACNV: allelic copy-number variation discovery from SNPs and coverage data
Authors: Chevalier Aaron , Lichtenstein Lee , Smirnov Andrey , Lee Samuel K. , Babidi Mehrtash , Benjamin David I. , Ruano-Rubio Valentin
Published: July 2017

The presence of somatic copy-number alterations in tumor genomes can be used to predict both patient sensitivity to treatments as well as outcomes. The inclusion of allelic data improves statistical power to detect copy-number events and allows for discovery of copy-neutral events. We present GATK ACNV, an allelic copy-number variation method built on the Genome Analysis Toolkit. ACNV is a tool for detecting somatic copy-number activity from whole exome and whole genome sequencing data by segmenting the genome into regions of constant copy number and estimating copy ratio and minor-allele fraction in those regions.

ACNV uses a novel probabilistic model to account for reference bias (optionally using a panel of normals), which improves the estimation of minor-allele fraction. We combine this with the coverage model from GATK CNV by segmenting with a unified hidden Markov model, improving the statistical power to detect copy-number variation.

We validate ACNV using a purity series of the cell line HCC1143 and cancer samples from The Cancer Genome Atlas. Our results show that ACNV is able to discover regions of somatic copy-number activity accurately and with high resolution in both whole exome and whole genome sequencing data.

Citation Format: Aaron Chevalier, Lee Lichtenstein, Andrey Smirnov, Samuel K. Lee, Mehrtash Babidi, David I. Benjamin, Valentin Ruano-Rubio. GATK ACNV: allelic copy-number variation discovery from SNPs and coverage 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 3581. doi:10.1158/1538-7445.AM2017-3581
Abstract 3595: Under-reporting of research biopsies in clinical trials in oncology
Authors: Parseghian Christine M. , Raghav Kanwal , Yao James , Ellis Lee M. , Tam Alda , Overman Michael J.
Published: July 2017

Purpose: Research biopsies are frequently incorporated into clinical trials in oncology, and are often a mandatory requirement for trial enrollment. However, limited information is available regarding the extent and completeness of research biopsy reporting.

Methods: We identified a cohort of therapeutic clinical trials wherein at least one image-guided non-diagnostic research biopsy was performed between 1/2005 and 10/2010 from a large interventional radiology database at MD Anderson Cancer Center. Study protocols were compared with the highest level of corresponding publication as a manuscript, registry report, or abstract.

Results: A total of 866 research biopsies were performed across 46 clinical trials (median 19 biopsies/trial). After a median follow-up time of 5.8yrs from study completion, 35 trials (76%) had published manuscripts (18 reported biopsy results), 8 (17%) had either a registry or abstract report (1 reported biopsy results), and 3 (7%) were not reported. In total, 19 trials (41%) reported biopsy results. Of these 19 trials, 6 (32%) trials under-reported the number of biopsies performed. Only 14 of 32 (42%) trials with mandatory research biopsies reported on these biopsies. Comments regarding biopsy quality/adequacy were reported in only 5 trials. Complications from these biopsies occurred in 39 pts (grade 3 in 6 pts) in 8 trials, but only 1 (13%) trial reported biopsy complications. Factors associated with better reporting of research biopsies are shown in the Table. When limited to only published manuscripts, results were unchanged. Academic sponsorship and a larger number of biopsies, especially serial biopsies, were associated with increased reporting of research biopsies.

Conclusion: Despite ethical obligations to report research biopsies, 59% of trials do not report on these biopsies. Although complications occur, they are rarely reported. Clinical trial design efforts to ensure that an adequate number of research biopsies are obtained may lead to improved reporting of research biopsy biomarker results.

VariableNTrials reporting biopsies (%)P-valueMandatory or optional biopsy1Mandatory (+/- optional)3314 (42)Optional135 (38)Total number of biopsies per trial0.002<10193 (16)10-302211 (50)>3055 (100)Trials with serial biopsies (No. of pts.)0.00011-5110 (0)>=51813 (72)Study sponsorship0.03Industry246 (25)Academic2213 (59)Clinical trial0.77Multicenter218 (38)Single center2511 (44)Phase of clinical trial0.51I or I/II3315 (45)II or III134 (31)

Citation Format: Christine M. Parseghian, Kanwal Raghav, James Yao, Lee M. Ellis, Alda Tam, Michael J. Overman. Under-reporting of research biopsies in clinical trials in oncology [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 3595. doi:10.1158/1538-7445.AM2017-3595
Abstract 3596: How many tumor indications should be initially studied in clinical development of next-generation immunotherapies
Authors: Chen Cong , Deng Qiqi , He Linchen , Mehrotra Devan , Rubin Eric H. , Beckman Robert A.
Published: July 2017

An experimental oncology immunotherapy may have the potential to be effective in a large number of tumor indications. Once a recommended Phase II dose (RP2D) is determined, under resource constraint, a natural strategy is to conduct Phase II proof-of-concept (POC) trials in two waves. A cohort of potential tumor indications is selected for the first wave investigation and the second wave investigation in a different cohort of tumor indications is initiated only after the drug has been demonstrated to be effective in the first wave. Immunotherapy development is a dynamic environment with rapidly evolving mechanistic understanding, constant flow of new data and frequent changes in the competitive landscape. How many tumor indications should be investigated in the first wave given the uncertainties? We attempt to answer this question by maximizing a benefit-cost ratio, defined to be the expected number of effective tumor indications correctly identified in the two waves divided by the expected total sample size for the POC trials in the two waves and the total sample size for the Phase III trials triggered by those with a positive outcome in the first wave. It is found that the optimal number of the first wave POC trials is in a range of approximately three to six, which may vary with the resource constraint but is otherwise robust to the key factors we have considered. A recommendation is made on how much resource should be invested in the first wave.

Citation Format: Cong Chen, Qiqi Deng, Linchen He, Devan Mehrotra, Eric H. Rubin, Robert A. Beckman. How many tumor indications should be initially studied in clinical development of next-generation immunotherapies [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 3596. doi:10.1158/1538-7445.AM2017-3596
Abstract 360: Leveraging a novel ITIM motif in GPCRs for targeted antibody design
Authors: Belcastro Lili T. , Jancina Anastasia , Adams Christina , Paulukinas Ryan D. , Moore Catherine C.
Published: July 2017

CXCR4, a chemokine GPCR, is essential for migration of neuronal, hematopoietic, and breast cancer cells during metastasis whereby CXCR4 dysregulation promotes migration and invasion. Following SDF stimulation, CXCR4 is phosphorylated on Ser/Thr residues which initiates adaptor recruitment, receptor desensitization, and trafficking to endocytic sites. Here we show that stimulation with gradient SDF, delays receptor phosphorylation and trafficking, leading to sustained signaling to a novel CXCR4-SHP2-ERK pathway. SHP2 is a tyrosine phosphatase implicated in HER2(+) and triple-negative breast cancers, whereby it transduces mitogenic and migratory signals driving hyperproliferation and invasion. SHP2 is recruited to tyrosine phosphorylated ITIM motifs (immmunoreceptor tyrosine-based inhibitory consensus motifs), a hallmark found in inhibitory immune receptors with little evidence in GPCRs. Here we identify an ITIM motif in CXCR4 that regulates both SHP2 binding and signaling. Specifically, we assessed if gradient SDF stimulation of CXCR4 1) delays receptor phosphorylation and trafficking, 2) sustains signaling to SHP2-ERK, 3) induces SHP2-dependent migration; and if CXCR4 Tyr mutation within the ITIM motif 4) maintains SDF gradient sensing ability, and 5) disrupts interaction with and signaling to SHP2. Our data demonstrate that gradient SDF delays receptor Ser/Thr phosphorylation and internalization thereby sustaining signaling to SHP2-ERK and driving SHP2-dependent migration. Furthermore, the ITIM mutant maintains SDF gradient sensing ability, but disrupts interaction with and signaling to SHP2. Our data support a working model that CXCR4 contains a functional ITIM motif which we are currently leveraging for targeted antibody design for use in migration studies of aggressive breast cancer cells with dysregulated CXCR4. These studies were supported by NIH grant GM-097718, PA Department of Health grant SAP4100057688, and the Milton Lev Memorial Faculty Research Fund.

Citation Format: Lili T. Belcastro, Anastasia Jancina, Christina Adams, Ryan D. Paulukinas, Catherine C. Moore. Leveraging a novel ITIM motif in GPCRs for targeted antibody design [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 360. doi:10.1158/1538-7445.AM2017-360
Abstract 3603: Optimizing combination therapy against antiestrogen-resistance in estrogen receptor positive breast cancer
Authors: Gutgesell Lauren M. , Xiong Rui , Zhao Jiong , Tonetti Debra A. , Thatcher Gregory R.
Published: July 2017

Approximately 75% of breast cancer incidences are Estrogen Receptor positive (ER+). Treatment of ER+ breast cancer with antiestrogen endocrine therapy targets the proliferative mechanisms of ER using selective ER modulators (SERMs), such as tamoxifen, and selective ER downregulators (SERDs), such as fulvestrant. The resistance to endocrine therapy, either innate or acquired, is clinically diagnosed in up to 50% of patients within 5 years of treatment. Antiestrogen therapy of ER+ mammary cancer cells in vitro and in xenografts does not cause complete cell death or regression. Through the use of combination therapy to target the remaining sub-population of cells, complete regression can be predicted. Our lab has developed endocrine tamoxifen-resistant models through prolonged exposure to tamoxifen, estrogen deprivation, and overexpression of PKCα, a pro-survival pathway component, in addition to a fulvestrant-resistant model through prolonged exposure to fulvestrant. Investigation of the resistance mechanisms will provide insight into potential, combinatorial targets for overcoming endocrine resistance in ER+ breast cancer. Use of spheroidal 3D cell culture provides a physiologically relevant model with sufficient throughput for drug discovery. Establishing spheroids and subsequent treatment predicts the efficacy of combination treatment on tumor regression. Targeting pathways associated with increased prevalence of resistance, such as CDK 4/6, can be employed for clinical therapy. Using both novel in-house and clinical SERMs and SERDs, we have used these multiple cell lines to discover combinatorial targets using both mechanistic and unbiased screening approaches. The use of combination endocrine therapy in tamoxifen-resistant models has shown antiproliferative synergy, and is able to enhance tumor regression in xenografts. By optimizing combinatorial endocrine treatment against both fulvestrant- and tamoxifen-resistance, novel therapeutic approaches are being developed for ER+ breast cancer.

Citation Format: Lauren M. Gutgesell, Rui Xiong, Jiong Zhao, Debra A. Tonetti, Gregory R. Thatcher. Optimizing combination therapy against antiestrogen-resistance in estrogen receptor positive 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 3603. doi:10.1158/1538-7445.AM2017-3603
Abstract 3605: The role of androgen receptor in invasive lobular breast carcinoma
Authors: Stires Hillary , Riggins Rebecca B.
Published: July 2017

The leading problem for women with estrogen receptor α (ER) breast cancer – approximately 70% of all breast cancers – is that while the majority of tumors initially respond to anti-estrogen treatment including Tamoxifen and aromatase inhibitors, they will develop endocrine resistance. A histological subset of breast cancer called invasive lobular carcinoma (ILC) accounts for 15% of all breast cancer cases and approximately 90% of ILC are ER-positive. Despite clinical markers suggesting a better prognosis for ILC compared to the more common invasive ductal carcinoma (IDC), recent data suggests women with ILC develop Tamoxifen resistance at a higher rate than IDC. New strategies for treating hormone refractory tumors are needed that not only overcome anti-estrogen resistance, but also present a more tolerable side effect profile and have fewer dose-limiting toxicities than adjuvant chemotherapy. The majority of ER-positive breast cancers also express androgen receptor (AR) and while AR presence in breast cancer is controversial, increased expression of AR leads to Tamoxifen resistance in IDC cell lines. Since ILC has more AR expression than IDC, the role of AR in ILC was studied by treating cells with the non-aromatizable androgen dihydrotestosterone (DHT) and the synthetic androgen R1881 as well as the anti-androgen Enzalutamide. We have previously begun to characterize a Tamoxifen resistant variant of the ILC cell line Sum44PE termed LCCTam cells. In both Sum44PE and LCCTam cells, AR protein expression increases in response to androgens, an action that is blocked by Enzalutamide. Interestingly, androgens do not promote growth in ILC cells, but Enzalutamide is still able to inhibit growth. These results suggest Enzalutamide may be an effective alternative therapy for women with ILC. Future studies will focus on whether regulation of nuclear receptor co-factors influences differences in AR signaling in ILC.

Citation Format: Hillary Stires, Rebecca B. Riggins. The role of androgen receptor in invasive lobular breast carcinoma [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 3605. doi:10.1158/1538-7445.AM2017-3605