bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1235: Repeated whole-exome sequencing for cell-free tumor DNA profiling of colon cancer patients: Searching for mechanisms of acquired chemoresistance
Authors: Vymetalkova Veronika , Pardini Barbara , Jiraskova Katerina , Urbanova Marjketa , Levy Miroslav , Veskrnova Veronika , Vodicka Pavel , Naccarati Alessio
Published: August 2018

Colorectal cancer (CRC) is a worldwide health burden with nearly 1.2 million new cases expected each year globally. When CRC is identified early, there is a five-year survival rate of about 90% but it drops to almost 12% once there are distant metastases. Drug resistance is a limiting factor of the efficacy of chemotherapy in CRC treatment. Significant efforts are currently being employed to discriminate patients who will benefit or not from chemotherapy. In fact, there is no current 'gold standard' to differentiate responders from non-responders. In the present work, we focused on good responders (those who benefit from the chemotherapy, not having side effects like toxicity, no relapses and having a complete response with no residual cancer) and non-/bad responders (patients with acquired chemoresistance and lack any response, or developing toxicity). The main aim was to identify markers/mutations in plasma cell-free DNA that could be associated with good/bad responders and chemoresistance. Paired plasma samples from colon cancer patients collected before and after therapy and the relative cell-free tumor DNA (ctDNA) was profiled by a whole exome sequencing approach in order to identify novel acquired mutations. Plasma ctDNA was isolated by QIAamp Circulating Nucleic Acid Kit. The SureSelectXT HS Reagent Kit was used for library preparation and libraries were sequenced by the HiSeq2500 system. Analysis was performed on nine patients (stage II and III) treated with the same 5-FU based therapy. The first sampling was collected at the time of diagnosis (i.e., active disease), and the second after 6-9 months depending on patient` s conditions (i.e., covering the tumor resection, administration of adjuvant chemotherapy). After follow up, three patients were classified as good responders and six as non/poor responders. The bioinformatics analysis is currently running. The number of total reads exceeded 990x106. Total length of all exons was 221,924,089bp. After trimming, the average read length was 113bp. Alignment to human reference genome (hg38) is > 99.8%. Coverage of exons ranges from 17 to 34. Results of the study will be presented during the meeting.

Supported by grant AZV MZ 17-30920A, 15-26535A and GACR 17-16857S.

Citation Format: Veronika Vymetalkova, Barbara Pardini, Katerina Jiraskova, Marjketa Urbanova, Miroslav Levy, Veronika Veskrnova, Pavel Vodicka, Alessio Naccarati. Repeated whole-exome sequencing for cell-free tumor DNA profiling of colon cancer patients: Searching for mechanisms of acquired chemoresistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1235.
Abstract 1281: Genomic structure variation in large screening for pediatric sarcoma therapy
Authors: Cheng Lijun , Chandra Pooja , Wang Limei , Pollok Karen , Pandya Pankita , Murray Mary , Carter Jacquelyn , Ferguson Michael , Reza Mohammad , Mark Mashall , Li Lang , Renbarger Jamie
Published: August 2018

Complex chromosomal aberrations such as amplification and deletion of DNA copy number are frequently seen in sarcoma. Fifty-five DNA structure variation has been listed as standard clinical diagnosis for sarcoma by standard of National Comprehensive Cancer Network (NCCN). However, copy number variation (CNV) as a biomarker of drug treatment for pediatrics sarcoma is still unclear, especially for relapsed and high recurrent patients of pediatric sarcoma. The paper aims to detect the prognosis biomarkers for rhabdomyosarcoma, Ewing's sarcoma (ES), and osteosarcoma based on copy number variation for 128 FDA-approved cancer drugs systematically. The 182 copy number variation (CNV) profiles from clinical sarcoma patients across three types of sarcoma, including osteosarcoma, rhabdomyosarcoma and ES, are observed. Cox survival regression model is used to select significant cancer-related CNVs systematically by correlation with overall survival analysis. 532 significant common CNVs and 782 specific CNVs for different types of sarcoma are observed by p-value <0.01. By comparing with healthy persons, COSMIC database, 947 cancer cells and our INHOUSE tumor datasets, 32 out of 532 CNVs for specific sarcoma types are validated. This systematic CNV comparison makes it possible to map DNA copy number changes and identify chromosomal regions containing “target genes” responsible for tumor development and/or progression. Integrating large-scale drug screening with copy number variation analysis on 38 sarcoma cancer cells, 95 out of 532 are confirmed as drugs resistance and sensitive biomarkers for different types of sarcoma. 15 chemotherapies show strong signals connecting with 42 biomarkers, including genes MYC, RAD21, and RB1 amplification. By bridging molecular biomarkers between tumors and sarcoma cell lines, 5 optimum drugs associated with 14 enzyme biomarkers are recommended for pediatric rhabdomyosarcoma, ES, and osteosarcoma treatment respectively. The research not only detects copy number variations both of sarcoma cell lines and tumors, but also provides novel insights into drug biomarkers based on copy number amplification or deletion for bone sarcoma and soft tissue sarcoma, respectively.

Citation Format: Lijun Cheng, Pooja Chandra, Limei Wang, Karen Pollok, Pankita Pandya, Mary Murray, Jacquelyn Carter, Michael Ferguson, Mohammad Reza, Mashall Mark, Lang Li, Jamie Renbarger. Genomic structure variation in large screening for pediatric sarcoma therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1281.
Abstract 1307: Effect of tumor purity on somatic mutation detection using next-generation sequencing technology: A benchmarking study
Authors: Jones Wendell , Xiao Wenming ,   Somatic Mutation Working Group, SEQC2 Consortium
Published: August 2018

Next generation sequencing (NGS) is becoming an essential tool for clinical cancer care. Whole genome sequencing (WGS), whole exome sequencing (WES), and targeted gene sequencing (TGS) have emerged as important tools and are critical for advancing precision oncology to meaningfully impact patient lives. To enable this goal, we must first thoroughly characterize the complexities of using NGS to identify somatic mutations in samples with tumor heterogeneity and variable tissue sample purity.

Here, we applied both experiment and in silico approaches to determine the effects of tumor heterogeneity on somatic mutation detection. First, we systematically investigated somatic mutation events in paired cell lines (breast carcinoma and matched normal) using a myriad of NGS platforms and protocols. Then, we applied machine learning algorithms to define high confidence mutation calls with datasets from the combination of all platforms and pipelines. Finally, we performed whole genome sequencing from tumor DNA samples titrated with matched normal cells to create a gradient of tumor purities from 100%, 75%, 50%, 20%, 10%, 5%, and 0%. We also created a series of in silico mixes by pooling reads from tumor and normal cell lines at respective ratios.

With somatic variation “ground truth” established by multiple orthogonal sequencing platforms and multiple analysis tools, we evaluated performance of individual software tools for tumor purity assessment and for mutation detection. Our experimental design allowed us to systematically evaluate accuracy, specificity and sensitivity of mutation detection across a range of tumor purities, as well as conduct a head-to-head comparison of in silico approaches versus experimental approaches.

This comprehensive study will help to clarify our understanding of experimental and analytical challenges that arise when confronted with tumor heterogeneity in patient care clinical decisions. In addition, data generated in this study will be used as a benchmark resource for the community to develop and improve tools to meet clinical challenges.

Citation Format: Wendell Jones, Wenming Xiao, Somatic Mutation Working Group, SEQC2 Consortium. Effect of tumor purity on somatic mutation detection using next-generation sequencing technology: A benchmarking study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1307.
Abstract 1369: Analysis of association between homologous recombination deficiency and tumor mutational burden in solid tumors
Authors: Li Hua , Wu Liqun , Shou Tao , Jiang Bo , Zhuang Li , Li Kunsong , Tan Xiang , Guo Chao , Guo Weidong , Guan Yan , Chen Zheng , Ding Xiao , Guo Jun , Du Zhenfang , Cui Qiang , Che Yue , Yao Ming
Published: August 2018

Background: Multiple types of tumors exhibit DNA repair dysfunction via homologous recombination deficiency (HRD) due to genetic and epigenetic alterations of HR pathway genes, including BRCA1/2, PALB2, ATM, ATR, CHK1/2, BARD1, BIRP1, MRE11A, RAD51 family and FANC family. Some studies showed that tumors with homologous recombination deficiency might result in more mutations than tumors with non-deficient HR. Accumulating evidence suggests that tumor mutational burden (TMB) evaluated by comprehensive genomic profiling was associated with the responses of immune checkpoint inhibitors in solid tumors.

Methods: FFPE tumor samples of 777 Chinese patients were collected for next-generation sequencing (NGS)-based targeted panel assay across multiple types of tumors, including lung, breast, soft tissue, gastrointestinal and gynecology cancers. There were 471 males (60.6%) and 306 females (39.4%) with a median age of 58 years old. Genomic alterations of HR-related genes and TMB values were assessed by next-generation sequencing assay, including single base substitution, short and long insertions/deletions, copy number variations, gene fusions and rearrangements.

Results: In total, 25% of the 777 solid tumor patients had at least one genomic alteration of the HR genes (N=197, HRD group). The top mutant HR genes included BRCA1/2 (28.8%), FANC family (27.6%), ATM (27.4%), ATR (11.2%), RAD51 family (8%), BARD1 (7.6%), PALB2 (7.1%), BIRP1 (5.6%), CHK1/2 (5.0%) and MRE11A (4.6%). TMB was 10.4 muts/Mb in the HRD group compared to 6.4 muts/Mb in the rest of the patients (p<0.01). In addition, 43.2% of the patients in the HRD group had TMB-high values, which was higher than in the non-HRD group at 22.8% (P<0.01). High TMB values were more commonly detected in the colorectal cancer patients.

Conclusions: Our study revealed that the solid tumors harboring HR gene mutation were more likely to have higher TMB values. BRCA1/2, FANC family and ATM were the most common mutant genes. CRC was the dominant cancer type showing high TMB values associated with HRD. Further analysis is warranted to investigate the association.

Citation Format: Hua Li, Liqun Wu, Tao Shou, Bo Jiang, Li Zhuang, Kunsong Li, Xiang Tan, Chao Guo, Weidong Guo, Yan Guan, Zheng Chen, Xiao Ding, Jun Guo, Zhenfang Du, Qiang Cui, Yue Che, Ming Yao. Analysis of association between homologous recombination deficiency and tumor mutational burden in solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1369.
Abstract 1553: Carcinoembryonic antigen (CEA) expression is regulated by mutant KAS in mucinous colon cancers
Authors: Kuracha Murali , Govindarajan Venkatesh , Loggie Brian W. , Thomas Peter
Published: August 2018

Purpose: Carcinoembryonic antigen (CEA/CEACAM5) is a marker and prognostic indicator for colorectal cancers (CRCs). CEA overexpression is also a major causative factor in the development of liver metastasis from a significant fraction of colorectal cancers (CRC) including mucinous adenocarcinomas (MCAs). Very little is known about the molecular mechanisms that regulate the expression of CEA in cancers in general and in CRCs in particular. This study tests the hypothesis that mutant KRAS, a frequently mutated gene in CRCs, regulates CEA expression in CRCs.

Methods: Mutant KRAS expression was reduced in two high CEA-expressing mucinous CRC cell lines, LS174T (KRAS G12D) and RW7213 (KRAS G12C), by short hairpin RNA (shRNA)-mediated knockdown using a lentiviral vector. Inducible and reversible knockdown of KRAS was achieved by addition or withdrawal of doxycycline. Alterations in activation of ERK-and PI3K-pathway effectors downstream of KRAS were assessed by Western blots. Two small-molecule inhibitors, pictilisib (GDC0941) and cobimetinib (GDC0973), were used to inhibit PI3K and MEK respectively.

Results: Knockdown of mutant KRAS in CRC cell lines reduced CEA expression. However, knockdown of wild-type RAS did not change CEA expression. Restoration of mutant KRAS reestablished CEA expression in both cell lines. This recovery of CEA expression was blocked by addition of the MEK inhibitor, cobimetinib or the PI3K inhibitor, picstilisib. Combined treatment with both inhibitors was more effective in reducing CEA expression than single-agent treatment.

Conclusions: Our results suggest that mutant KRAS, through engagement of MEK-ERK and PI3K-AKT signaling pathways, regulates CEA expression in CRCs. CEA has been implicated in the development of lung and liver metastasis from CRCs, by reacting with stromal cells and altering the tumor microenvironment. Our results therefore, suggest a potential vulnerability that could be exploited for antimetastatic therapy.

Citation Format: Murali Kuracha, Venkatesh Govindarajan, Brian W. Loggie, Peter Thomas. Carcinoembryonic antigen (CEA) expression is regulated by mutant KAS in mucinous colon cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1553.
Abstract 160: Novel strategy targeting breast cancer stem cells CD44+/CD24-low responsible for breast cancer progression
Authors: Abouelnazar Fatma A. , Sultan Ahmed S.
Published: August 2018

The present study has been designed to isolate the highly tumorigenic sub-population of cells from the breast cancer cell line (T47-D). The effect of Manuka honey (MH), Frankincense essential oil (F), Metformin (M) and combined treatment on eradicating breast cancer stem cells (BCSCs) that are responsible for cancer progression was investigated.

The isolated (BCSCs) were subjected to different concentrations of (MH), (F), (M) and combined treatment to visualize their effects on BCSCs viability, morphological changes, caspase-3 activity, apoptosis induction, clonogenic survival, β-catenin, ALDH6A1, Notch-1, Notch-4 and Nonog protein expression, using western blot analysis and protein localization by immunocytochemical technique.

Inhibited viability of isolated breast cancer stem cells, which showed apoptotic morphological changes were observed beside increased caspase-3 activity and inhibited clonogenic survival compared to control. At the protein level, our data showed that (MH), (F), (M) and combined synergistic treatment decreased the expression of β-catenin levels, ALDH6A1 and Notch-1 compared to control. In addition, (MH) showed no effect on Notch-4 expression, but significantly decreased the expression level of Nanog. In contrast, (F) treatment enhanced the protein expression of Nanog level in a dose dependent manner compared to control. Furthermore, (MH), (F), (M), and combined treatment showed conspicuously decrease in the nuclear and cytoplasmic level of β-catenin and ALDH6A1 of CD44+/CD24-low (BCSCs) compared to control.

Taken together, natural compounds of Manuka honey and Frankincense essential oils and their combination with Metformin have been emerged as a potential strategy to target and eradicate (BCSCs).

Citation Format: Fatma A. Abouelnazar, Ahmed S. Sultan. Novel strategy targeting breast cancer stem cells CD44+/CD24-low responsible for breast cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 160.
Abstract 1736: The combination of CXCR4 and checkpoint receptor inhibition improves survival in an orthotopic murine glioma model
Authors: Wu Adela , Cardarelli Pina , Oyasu Miho , Menezes Daniel , Ponath Paul , Cogswell John , Maxwell Russell , Luksik Andrew , Hung Alice , Kim Eileen , Belcaid Zineb , Brem Henry , Pardoll Drew , Lim Michael
Published: August 2018

Introduction: Angiogenesis plays an important role in the malignancy of glioblastoma (GBM) as well as in cancer immunotherapy. In addition, PD-1 checkpoint receptors are upregulated in GBM. We investigate the treatment effects of combination immunotherapy with checkpoint inhibitor anti-PD-1 and anti-CXCR4, an antagonist of a chemokine receptor involved in immune cell homing as well as vasculature development, in a murine glioma model.

Methods: C57Bl/6 mice were implanted with GL261-Luc+ glioma cells and randomized into 4 treatment arms: 1) control, 2) anti-PD-1 monotherapy, 3) anti-CXCR4 monotherapy, and 4) combination anti-PD-1 and anti-CXCR4 therapy. Overall survival and median survival were assessed. Brain samples from untreated mice were stained for CXCR4 expression on plasma membrane, and immunohistochemistry studies were conducted on human glioblastoma specimens as well. Immune cell activation and cell population changes were assessed through flow cytometry analysis.

Results: Both murine and human glioma specimens demonstrated robust positive expression of CXCR4 on tumor-infiltrating immune cells and endothelial cells of vasculature specific to the tumor bed. Combination therapy with anti-PD-1 and anti-CXCR4 conferred survival benefit compared to control and both monotherapy arms. Long-term survivors that had received combination therapy demonstrate immune memory and decreased populations of immunosuppressive, tumor-promoting immune cells. For instance, the monocytic myeloid-derived suppressor cell population was decreased in the brain in mice treated with combination therapy. The pattern of change in microglia was similar in the brain compartment for the combination treatment group as well.

Conclusion: Anti-CXCR4 and anti-PD-1 synergistic immunotherapy not only modulates the immune cell make-up of the glioma microenvironment but also affects vasculature within the tumor region. Dual therapy targeting both checkpoint and chemokine receptors results in improved survival rates.

Citation Format: Adela Wu, Pina Cardarelli, Miho Oyasu, Daniel Menezes, Paul Ponath, John Cogswell, Russell Maxwell, Andrew Luksik, Alice Hung, Eileen Kim, Zineb Belcaid, Henry Brem, Drew Pardoll, Michael Lim. The combination of CXCR4 and checkpoint receptor inhibition improves survival in an orthotopic murine glioma model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1736.
Abstract 1770: Morab-202, a folate receptor alpha-targeted antibody-drug conjugate, shows a highly potent activity against a panel of FRA-expressing tumors
Authors: Mignard Caroline , DURIX Coralie , Rybinski Katherine , Cheng Xin , Furuuchi Keiji , Albone Earl , Uenaka Toshimitsu , Boisferon Marc Hillairet de
Published: August 2018

Folate receptor alpha (FRA) is a membrane protein with high affinity for binding and transporting folate into cells. Overexpression of FRA may confer a growth advantage to tumors by increasing folate uptake and affecting cell proliferation via alternative cell signaling pathways (1). FRA levels have been found to be elevated in tumors of epithelial origin compared to normal tissue as cancers of the breast (including TNBC (2)), colon, lungs and ovary (3).

In this study, we report the development of MORAb-202, an anti-FRA antibody-drug conjugate (ADC), consisting of a FRA-binding antibody (MORAb-003, farletuzumab) with a cathepsin-cleavable form of eribulin (eribulin mesylate, marketed as Halaven®), a highly potent anti-mitotic agent that induces cell-cycle arrest and cell death by targeting microtubules.

We first study expression of FRA on a large panel of tumors patient-derived xenograft (PDX) and Cancer Cell Line-derived Xenograft (CDX). Then, we performed in vitro and in vivo anti-proliferation assays and compare antitumor activity of MORAb-202 with free eribulin accordingly to the FRA expression level. FRA expression was found to be determinant in the sensitivity of tumor cells to the cytotoxic effect of the ADC. Moreover, in case of high expression of FRA, MORAb-202 showed a higher antitumor activity compared with free eribulin.

These results suggest that FRA expression could be used as a response-predictive biomarker for this targeted therapy. The ability to identify and treat patients with an effective therapy based on the known expression of the tumor marker is a key point in predictive medicine progress. These findings support the clinical development of MORAb-202 ADC as a novel targeted therapy for patients with FRA-expressing tumors.

The ADC described in this abstract is investigational, as efficacy and safety have not been established. There is no guarantee that this ADC will be available commercially.

1-Siu MK et al., PLoS One. 2012;7(11) 2-Nacela BM. et al., PLoS One. 2015, 10(3) 3-Cheung A. et al., Oncotarget. 2016 7(32), 52553-52574 4-Arrowsmith J. & Miller P. 2011-2012. Nat. Rev. Drug Discov. 12, 569 (2013). 5-Paul S.M. et al. Nat. Rev. Drug Discov. 9, 203-214 (2010). 6-Hidalgo, M. et al. Cancer Discov. 4, 998-1013 (2014).

Citation Format: Caroline Mignard, Coralie DURIX, Katherine Rybinski, Xin Cheng, Keiji Furuuchi, Earl Albone, Toshimitsu Uenaka, Marc Hillairet de Boisferon. Morab-202, a folate receptor alpha-targeted antibody-drug conjugate, shows a highly potent activity against a panel of FRA-expressing tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1770.
Abstract 1845: TP53 status determines the fate of cancer cells exposed to ionizing radiation and DNA-PK inhibitor, M3814
Authors: Sun Qing , Guo Yige , Liu Xiaohong , Czauderna Frank , Zenke Frank , Blaukat Andree , Vassilev Lyubomir T.
Published: August 2018

Inhibition of DNA double strand break repair in cancer cells has been proposed as a new therapeutic approach for potentiation of radiotherapy. M3814 is a potent and selective inhibitor of DNA-PK, a key component of non-homologous end joining repair pathway and is currently under clinical investigation in radiation combination trials. We studied the mechanism of cancer cell response to combined treatment with ionizing radiation and M3814 using cancer cell lines with different p53 status. M3814 blocked the repair of radiation-induced DSBs and suppressed a negative regulatory loop between DNA-PK and ATM causing enhanced phosphorylation and activation of ATM. In the p53 wild-type cells, ATM and its targets, CHK2 and p53, were activated more strongly by the combination treatment than by radiation alone, leading to a complete p53/CHK2-dependent cell cycle block and premature cell senescence. The p53-null or mutant cancer cells were unable to fully arrest the cell cycle and a substantial fraction entered S phase with unrepaired DNA, leading to mutations, chromosomal aberrations, aneuploidy, micronucleation and ultimately cell death, primarily due to mitotic catastrophe. Two isogenic pairs of p53 null/wt cells (A549 and HT-1080) were generated and used to demonstrate the critical role of p53 in the choice of M3814-modified radiation response. Time-lapse imaging of cell death kinetics using a small panel of p53 wild-type and p53 null/mutant cancer lines revealed clear differences in outcome dependent on p53 status. However, standard growth/viability assays failed to show a role of p53 in the response type, due to inability to discriminate between cell cycle arrest and cell killing. Similarly, screening results obtained from large cancer cell panels (>100 lines) did not identify p53 as a marker of response. Our data revealed an important role of p53 in determining the mode of cancer cells' response to radiation in the presence of M3814 and suggest that p53 mutation status should be considered in the design of clinical trials. The failure of standard growth/viability screens with large cancer cell line panels to identify p53 status as a response indicator raises an alert for the utility of these screening platforms currently widely used in cancer drug discovery and development.

Citation Format: Qing Sun, Yige Guo, Xiaohong Liu, Frank Czauderna, Frank Zenke, Andree Blaukat, Lyubomir T. Vassilev. TP53 status determines the fate of cancer cells exposed to ionizing radiation and DNA-PK inhibitor, M3814 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1845.
Abstract 1888: The FAD-directed LSD1 specific inhibitor, INCB059872, is a promising epigenetic agent for AML therapy by inducing differentiation of leukemic stem/progenitor cells
Authors: Chadderton Antony , Ye Min , Diamond Melody , Roman Valerie , Weber Michael , He Chunhong , Wu Liangxing , Yeleswaram Swamy , Roberts Alan , Yao Wenqing , Hollis Gregory , Huber Reid , Scherle Peggy , Ruggeri Bruce , Lee Sang Hyun
Published: August 2018

Numerous studies have elucidated that the most pivotal functions of lysine specific demethylase-1 (LSD1) are associated with regulating normal or malignant hematopoiesis by maintaining stem cell self-renewal and regulating myeloid differentiation. In preclinical models, studies with either pharmacological inhibition or genetic knockdown of LSD1 demonstrated that LSD1 is essential for differentiation of progenitor cells during normal hematopoiesis. In the clinic, AML manifests itself via clonal expansion of abnormal differentiation and proliferation of myeloid cells and, therefore, the inhibition of LSD1 activity with small molecule inhibitors could be a promising therapeutic approach for AML. Previously, we reported upon the identification of a flavin adenine dinucleotide (FAD) directed LSD1 specific inhibitor, INCB059872, which is efficacious in preclinical mouse models utilizing human AML cell lines and primary AML cells by inducing cell differentiation as indicated by the induction of CD11b and CD86 markers. Using a larger panel of myeloid and HSC flow cytometry markers, our currents efforts expanded upon these observations to ascertain whether INCB059872 enhanced lineage commitment at hematopoietic stem cell (HSC) and/ or promoted monocytic/granulocytic differentiation of human primary AML cells ex vivo and in human systemic AML PDX models. In both human AML PDX models and human primary AML samples, INCB059872 increased myeloid differentiation with increasing populations of monocytes (CD14+) and granulocytes (CD15+). Furthermore, INCB059872 induced the differentiation of early hematopoietic progenitors, CD34+/CD38- to more committed CD34+/CD38+ multipotent/oligopotent progenitors, which in turn gave rise to lineage specific progenitors in the human AML PDX models. These studies support further exploration of INCB059872 as a promising novel epigenetic agent for AML therapy whose mechanism of action lies in part through the induction of differentiation of leukemic stem/progenitor cells to more committed hematopoietic lineages.

Citation Format: Antony Chadderton, Min Ye, Melody Diamond, Valerie Roman, Michael Weber, Chunhong He, Liangxing Wu, Swamy Yeleswaram, Alan Roberts, Wenqing Yao, Gregory Hollis, Reid Huber, Peggy Scherle, Bruce Ruggeri, Sang Hyun Lee. The FAD-directed LSD1 specific inhibitor, INCB059872, is a promising epigenetic agent for AML therapy by inducing differentiation of leukemic stem/progenitor cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1888.
Abstract 19: Trastuzumab resistance accompanies vasculogenic mimicry in HER2-positive breast cancer cells
Authors: Shimoda Masafumi , Hori Ami , Noguchi Shinzaburo
Published: August 2018

Trastuzumab (Tzm) is a drug that targets HER2/ERBB2/Neu, and is essential for the treatment of HER2-positive breast cancer. However, resistance to the drug is a major obstacle in controlling the progression of this devastating disease. We hypothesized that Tzm load might induce a phenotypic change in HER2-positive breast cancer cells, enabling them to escape and survive Tzm activity. We conducted comprehensive immunophenotyping to detect the phenotypic changes in HER2-positive breast cancer cells loaded with Tzm, and compared the immunophenotype of Tzm-loaded cells with that of control cells based on the criteria determined a priori. Out of 242 cell surface antigens, 9 antigens were significantly upregulated and 3 were significantly downregulated. Surprisingly, all the antigens were related to endothelial and stem cell phenotypes, suggesting that Tzm load induced vasculogenic mimicry (VM). Moreover, we found VM markers like COX2, MMP2, MMP14, phospho-SMAD2/3, VEGFA, HIF1A, and TWIST1 to be upregulated in Tzm-loaded cells. However, Tzm-loaded cells did not exhibit tube formation on Matrigel, a hallmark of VM. Since the Tzm-loaded cells were still sensitive to Tzm, we used three Tzm-resistant cell lines to investigate if Tzm resistance accompanied VM. All Tzm-resistant cell lines exhibited tube formation on Matrigel. Importantly, several growth factors including EGF, FGF2, IGF1, and VEGF promoted VM in these cells, suggesting that single molecular-targeted drugs did not effectively inhibit VM as other growth factors could quickly compensate the VM pathways. We then examined if eribulin, a tubulin-binding chemotherapeutic drug that promotes vascular remodeling, inhibited VM in Tzm-resistant cells. Eribulin inhibited tube formation in Tzm-resistant cells at a clinically relevant concentration. In conclusion, Tzm load induces an incomplete vasculogenic phenotype in HER2-positive breast cancer cells. The cells exhibit VM after eventually acquiring Tzm resistance. Since VM drives metastasis, its regulation in Tzm-resistant HER2-positive breast cancer appears to be a promising approach in suppressing the progression of HER2-positive breast cancer.

Citation Format: Masafumi Shimoda, Ami Hori, Shinzaburo Noguchi. Trastuzumab resistance accompanies vasculogenic mimicry in HER2-positive breast cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 19.
Abstract 1911: Uncovering novel targets of recurrent glioblastoma using transcriptomic profiling in a patient-derived xenograft model
Authors: Yelle Nicolas , Chokshi Chirayu , Vora Parvez , Brown Kevin R. , Qazi Maleeha A. , Singh Mohini , Adams Jarrett J. , Venugopal Chitra , Sidhu Sachdev , Moffat Jason , Singh Sheila K.
Published: August 2018

Glioblastoma (GBM) is the most common and aggressive adult primary brain tumor feared for its near uniformly fatal prognosis despite advances in multimodal therapy including surgical resection, chemotherapy and radiation. Poor patient survival due to tumor relapse is thought to be linked to intratumoral heterogeneity (ITH), driven by various environmental cues including chemotherapy and radiation treatment. ITH can be explained at the cellular level by the existence of multiple populations of cancer cells, including cancer stem cells (CSCs), which have acquired stemness properties like self-renewal, proliferation, and multilineage differentiation. In brain tumors, CSCs or brain tumor initiating cells (BTICs), have been shown to be resistant to both chemotherapy and radiation treatment, allowing them to escape therapy and allowing for tumor recurrence. To profile ITH as it evolves through therapy delivery, we have developed a novel and dynamic BTIC patient-derived xenograft (PDX) model of treatment-refractory human GBM, allowing for multimodal profiling of GBM BTICs through tumor engraftment, remission, and recurrence. In this study, we present the transcriptomic profiling at each stage, and novel target selection and validation through CRISPR/Cas9 knockouts, well-established in vitro stem cell assays, and in vivo characterization of their tumor initiation, development, and maintenance properties. Despite the fact that the BTIC population is responsible for GBM recurrence and thus patient demise, it remains a largely unknown landscape. Consequently, therapies that focus on targeting the BTIC compartment within the bulk tumor would provide better treatment and prognosis for patients with brain tumors. The study we present provides a unique therapeutic window into the recurrence of GBM, which drives patient mortality, yet is profiled far less than primary treatment-naïve GBM.

Citation Format: Nicolas Yelle, Chirayu Chokshi, Parvez Vora, Kevin R. Brown, Maleeha A. Qazi, Mohini Singh, Jarrett J. Adams, Chitra Venugopal, Sachdev Sidhu, Jason Moffat, Sheila K. Singh. Uncovering novel targets of recurrent glioblastoma using transcriptomic profiling in a patient-derived xenograft model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1911.
Abstract 2012: The generation of a NSCLC EMT reporter cell line for metastatic lung cancer drug discovery and development
Authors: Enuameh Metewo S. , Kumari Sangeeta , Zou Chauzhong , Foulke John , Turner Elizabeth , Shu Weiguo , Newman Robert
Published: August 2018

Cancer metastasis continues to be the leading cause of mortality in cancer patients around the world. One of the prominent biological processes implicated in cancer metastasis is epithelial-to-mesenchymal transition (EMT). EMT has also been shown to have roles in many aspects of cancer initiation and progression, including tumorigenesis and drug resistance. Despite the accumulation of a large body of data on the association of EMT with cancer, to date, EMT has not been an active target for therapeutic development partly due to the lack of appropriate in vitro models. Utilizing some of the basic biology of EMT, we have created a novel advanced in vitro model for use in both basic research and discovery of new anti-EMT drugs.

In lung cancer, vimentin (VIM) intermediate filament (IF) proteins are associated with EMT, and the metastatic spread of cancer. Vimentin expression is generally upregulated when epithelial cells transition to the mesenchymal phenotype. We capitalized on this biological phenomenon, using CRISPR/Cas9 gene editing to generate a VIM RFP (red fluorescent protein) reporter cell line in the A549 non-small cell lung cancer (NSCLC) cell line; one of the most widely used and recognized lung cancer cell lines. The A549 VIM RFP cell line harbors a C-terminal red fluorescent protein (RFP) tag on the vimentin gene which enables end-point or real-time tracking of the EMT status as cells transition from epithelial to mesenchymal phenotype under defined conditions. The EMT reporter cell line was verified at the nucleic acid (genomic and mRNA) and protein levels as well as in cell-based assays. Bio-functional evaluation of the A549 VIM RFP cell line shows sensitivity to metastatic NSCLC drugs PP1 (SRC inhibitor) and A83-01 (ALK5 inhibitor). These results provide the foundation for the use of this cell line in high throughput screening (HTS) applications including the identification of new anti-EMT drugs for metastatic NSCLC. Furthermore, the A549 Vim RFP reporter cell line is also a convenient and sensitive model for basic science research on the mechanisms of metastasis.

Citation Format: Metewo S. Enuameh, Sangeeta Kumari, Chauzhong Zou, John Foulke, Elizabeth Turner, Weiguo Shu, Robert Newman. The generation of a NSCLC EMT reporter cell line for metastatic lung cancer drug discovery and development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2012.
Abstract 2042: Hypoxia induces miR-153 through the IRE1α-XBP1 pathway to fine-tune the HIF1α/VEGFA axis in breast cancer angiogenesis
Authors: Liang Huichun , Zhou Zhongmei , Chen Ceshi
Published: August 2018

It is well documented that hypoxia activates the hypoxia-inducible factor (HIF1α)/vascular endothelial growth factor A (VEGFA) axis to promote angiogenesis in breast cancer. However, it is unclear how this axis is negatively regulated. A number of studies suggest that miR-153 inhibits tumor growth and metastasis by targeting SNAI1, ZEB2, MTDH, ADAM19, AKT1, HECTD3, and MCL1. We recently reported that miR-153 was induced by mifepristone and inhibited the breast cancer stem cells by down-regulating KLF5. In this study, we demonstrated that miR-153 directly inhibits expression of HIF1α by binding to the 3'UTR of HIF1A mRNA, as well as suppresses tube formation of primary human umbilical vein endothelial cells (HUVECs) and breast cancer angiogenesis by decreasing the secretion of VEGFA. Importantly, expression of miR-153 was induced by hypoxia-stimulated ER stress, which activates IRE1α and its downstream transcription factor XBP1. XBP1 directly binds to the promoter of the miR-153 host gene PTPRN and activates transcription. These results indicate that hypoxia induces miR-153 to fine tune the HIF1α/VEGFA axis in breast cancer angiogenesis and miR-153 could be used for breast cancer anti-angiogenesis therapy.

Citation Format: Huichun Liang, Zhongmei Zhou, Ceshi Chen. Hypoxia induces miR-153 through the IRE1α-XBP1 pathway to fine-tune the HIF1α/VEGFA axis in breast cancer angiogenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2042.
Abstract 2247: Accelerating cancer research using big data with BioKDE platform
Authors: Pang Xiaodong , Bou-Dargham Mayassa J. , Liu Yuhang , Cui Zihan , Sha Linlin , Zhao Tingting , Zhang Jinfeng
Published: August 2018

Large volumes of data have been generated in biomedical field every day and made publicly accessible. A significant portion of the data are highly under-analyzed. On the other hands, biomedical researchers having problems that can be solved by these data do not have the expertise to access and analyze the data. The BioKDE (Biomedical Knowledge Discovery Engine) platform aims to bridge this gap by accelerating biomedical discovery through integration and mining of large volumes of public genomic data. We have integrated a large volume of genomics data from TCGA (the Cancer Genome Atlas) and GEO (Gene Expression Omnibus) database, which are linked with patient clinical information. Powerful and versatile query functions were built for the integrated data. Basic and advanced analysis tools have been implemented with user-friendly interfaces. Pipelines can be built by chaining the query tools with analysis tools to perform sophisticated data acquisition and analysis tasks very conveniently. Pipelines can be saved and shared among researchers to quickly replicate certain analyses using the same dataset or different datasets. A large number of novel discoveries have been made, which can be used directly to write scientific research papers using these discoveries alone or by combining with additional experimental validation studies. We will present a few case studies published recently to illustrate the power of the BioKDE. We are looking for collaborators to write papers together for the discoveries we made. The platform can be accessed at http://www.insilicom.com.

Citation Format: Xiaodong Pang, Mayassa J. Bou-Dargham, Yuhang Liu, Zihan Cui, Linlin Sha, Tingting Zhao, Jinfeng Zhang. Accelerating cancer research using big data with BioKDE platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2247.
Abstract 2250: Tumor mutational burden: Guidelines for derivation and robustness of measurement
Authors: Mola Natalie , Schu Matthew , Stiegelmeyer Suzy , Jones Wendell , Weigman Victor J.
Published: August 2018

Tumor mutational burden (TMB) is defined as the number of somatic mutations per Mb of the genome and is used to represent accumulation of somatic mutations over the life of the tumor. Recent evidence has shown that high TMB scores are associated with improved response to immune therapies across multiple indications. However, the derivation of this score is not well characterized, nor is this score universally performed across laboratories.

Here we describe our methodology for calculating TMB, which considers an estimation of true germline mutations, the efficacy of different somatic callers, and the identification of regions within a capture panel that most reliably contribute to robust TMB scoring. To accomplish this, we only include positions that fall within high confidence regions of the genome as defined by NIST GIAB datasets HG001-HG005 v3.3.2. The high confidence regions encompass 88% of the exome.

Somatic variant calling is performed utilizing the tumor and normal samples using only positions where there is sufficient depth of coverage in both samples. Any remaining germline variants are excluded, leaving only somatic variants in the targeted, high-confidence regions for the final TMB calculation. TMB calculations utilizing high-confidence regions reduce the contribution of false positive variants in the mutational burden estimate.

We have compared TMB scores using this approach to those provided from evaluating somatic calls from TCGA, where matched tumor/normal pairs exist. In addition, we introduce a method to determine the effect on TMB scores when in silico determination of germline variants is used to derive somatic calls when matching normal samples are not available.

Defining the robustness of this score across and criteria for its derivation will help better position defining analytical range and future utility across indications and NGS panels

Citation Format: Natalie Mola, Matthew Schu, Suzy Stiegelmeyer, Wendell Jones, Victor J. Weigman. Tumor mutational burden: Guidelines for derivation and robustness of measurement [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2250.
Abstract 2620: Aquaporin 11 as a new predictive biomarker of overall survival and platinum-based chemotherapy response in lung adenocarcinoma patients
Authors: Sharpnack Michael , Carbone David P. , Dikov Mikhail M. , Tchekneva Elena E.
Published: August 2018

Background: Biomarkers predictive of response to chemotherapy are critically needed for the precise selection of treatment protocols in lung adenocarcinoma (LUAD). Aquaporins (AQPs), transmembrane water channels, are emerging targets in cancer. Recently discovered, non-ubiquitous family member aquaporin 11 (AQP11), a tissue-specific endoplasmic reticulum (ER) resident, was identified as a cellular pro-survival factor implicated in the maintenance of ER homeostasis. AQP11 is mapped to 11q13-q14 amplicon harboring oncogenic drivers and associated with poor prognosis in cancer patients. We recently showed that high AQP11 expression is an in-vitro therapeutic biomarker of cisplatin therapy, which directly interferes with AQP11 functional structure. In addition, silencing of AQP11 expression in human lung cancer cell lines significantly increased response to cisplatin treatment. We hypothesized that LUAD tumors expressing high levels of AQP11 depend on AQP11-mediated cytoprotection and would be more responsive to platinum-based chemotherapy targeting AQP11. Method: We downloaded and curated matched mRNA expression, survival, and drug response data from The Cancer Genome Atlas (TCGA) LUAD dataset (N=369). Results: Analysis of PRECOG and TCGA databases showed that high AQP11 mRNA expression is negatively prognostic in patients with LUAD. TCGA LUAD cases were categorized by AQP11 mRNA levels into high and low expression (high = AQP11 mRNA expression mean + 1 standard deviation). Patients with high tumor AQP11 mRNA expression (10.3%) had significantly worse overall survival (OS) compared to patients with low AQP11 expression (p=0.0015). An analysis of patients treated with platinum-based chemotherapy (N=74) showed that patients with high AQP11 mRNA expression (7%) had significantly higher OS then patients with LUAD expressing low levels of AQP11 (p=0.0263). Conclusions: This study identifies AQP11 as a new biomarker of OS and chemotherapy in LUAD patients. It is conceivable that lung tumors expressing high levels of AQP11 are dependent on its function and elevated AQP11 expression renders tumor resistance to microenvironment and therapy-induced stress and associates with lower OS of patients. At the same time, as cisplatin efficiently targets AQP11 functional multimeric structure, these AQP11-depending tumors are more prone to platinum based chemotherapy. This study provides a rationale for combination anti-AQP11 and chemotherapy in LUAD tumors with high AQP11 expression.

Citation Format: Michael Sharpnack, David P. Carbone, Mikhail M. Dikov, Elena E. Tchekneva. Aquaporin 11 as a new predictive biomarker of overall survival and platinum-based chemotherapy response in lung adenocarcinoma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2620.