bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract KN03: Keynote Lecture: Cell transfer immunotherapy targeting unique somatic mutations in cancer
Authors: Rosenberg Steven A. 
Published: August 2018

Abstract
Adoptive cell transfer (ACT) immunotherapy using T lymphocytes with antitumor activity is a living therapy that can be highly effective in patients with a variety of metastatic cancers. Naturally occurring tumor-infiltrating lymphocytes (TIL) expanded in vitro and administered following a lymphodepleting preparative regimen mediated objective regression of metastatic melanoma in 56% of 194 patients, including complete regressions in 20% of patients who remain ongoing disease-free 3 to 10 years later. To determine the antigens recognized by TIL we developed an approach based on deep exomic sequencing of the cancer and immunologic testing of TIL or peripheral lymphocytes to generate T cells that recognized immunogenic mutations. TIL from 34 patients with metastatic melanoma recognized 78 random somatic mutations, none of which were shared among different melanomas. We next extended these studies to patients with common epithelial cancers and showed that 64 of 84 (70%) patients with a variety of human cancer types, including esophageal, colorectal, bile duct, gastric, pancreatic, ovarian, cervical, and lung cancer, contained T cells that recognized 142 neoantigens, all of which were unique except for KRAS (3 patients) and p53 (4 patients). Targeting unique cancer mutations has extended the reach of ACT immunotherapy and was used to mediate objective regressions in selected patients with chemorefractory metastatic cancers of the bile duct, colon, cervix, and breast. In addition to the use of naturally occurring mutation-reactive cells, we have genetically engineered autologous lymphocytes to express antitumor T-cell receptors (TCR) or chimeric antigen receptors (CAR) for use in ACT immunotherapy that can mediate durable cancer regressions in heavily pretreated patients with refractory lymphomas, sarcomas, and melanoma. Autologous T-cells can be used to provide a highly personalized immunotherapy for cancer patients refractory to conventional cancer treatments.
Citation Format: Steven A. Rosenberg. Keynote Lecture: Cell transfer immunotherapy targeting unique somatic mutations in cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr KN03.
Abstract LB-A18: Targeting the WNT-pathway in 3D-cultured in vitro PDX models for pancreas cancer
Authors: Dijkmans Thomas , Herpers Bram , Basten Sander , Yan Kuan , Giesemann Torsten , Schueler Julia , Price Leo 
Published: August 2018

Abstract
Creating patient-derived xenograft (PDX) models from human cancers allows bio-banking, propagation, characterization and drug testing on a large panel of tumor variants. To scale up the number of compound tests, identify relevant compound doses, increase the throughput, and study relevant cancer-driving pathways we developed 3D in vitro culture methods for PDX model-derived cell isolates. In this effort, each individual model is subjected to a wide panel of culture medium formulations, amongst which some media contain WNT-pathway stimulating components.
We identified an absolute dependency of a pancreatic in vitro PDX tumor to the WNT-signaling potentiating factor R-Spondin, while other pancreas tumors showed little or no dependency. To further study the dependency of pancreatic PDX tumors on the functionality and signaling of the WNT-pathway, we exposed in vitro PDX cultures to increasing doses of anti-FZD7, anti-FZD8 and to the Porcupine inhibitor LGK974, which blocks WNT palmitoylation and therefore secretion.
Our findings are that the WNT-pathway is functional and contributing to pancreas cancer outgrowth and morphological differentiation to different extents in different patient-models. Our in vitro PDX culture system in combination with 3D phenotypic analysis allows in-detail study of the WNT-pathway, as well as by supplementation or omission of secreted factors, addition of small molecule inhibitors and by exposure to antibodies. These in vitro PDX models can be used to test novel compounds and antibodies targeting the WNT-pathway and underscore the WNT-pathway as a potential target in pancreatic cancer.
Citation Format: Thomas Dijkmans, Bram Herpers, Sander Basten, Kuan Yan, Torsten Giesemann, Julia Schueler, Leo Price. Targeting the WNT-pathway in 3D-cultured in vitro PDX models for pancreas cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr LB-A18.
Abstract 1059: EpCAM differentially expressed on circulating and disseminated tumor cells promotes tumor metastasis in breast cancer patients
Authors: Lin Peter P. , Li Junjian , Wang Daisy , Gires Olivier , Wang Hongxia 
Published: August 2018

Abstract
To investigate the role of EpCAM expressed on both circulating tumor cells (CTCs) in peripheral blood and disseminated tumor cells (DTCs) in bone marrow with respect to tumor metastases, the integrated subtraction enrichment and immunostaining-FISH (SE-iFISH) was performed to quantify, phenotypically and karyotypically characterize cytogenetically abnormal CTCs and DTCs expressing EpCAM in breast cancer patients. In a cohort of 34 recruited late stage patients, consisting of 32 metastatic and 2 non-metastatic subjects, the average number of detected CTCs in metastatic vs non-metastatic patients was 25 and 18 cells, respectively. Among those CTCs in metastatic subjects, 23.4% of them showed EpCAM+, whereas none of EpCAM+ CTCs was detected in non-metastatic patients. There were total of 49 CTC clusters detected in metastatic patients, and 33% of those clusters were EpCAM+, however, only 3 CTC clusters were found in non-metastatic patients, and none of them was EpCAM+. In the case of DTCs, the average number of 2224 and 364 DTCs per subject was detected in metastatic vs non-metastatic subjects, with EpCAM+ ratio of 66.53% in metastatic and 8% in non-metastatic patients. Analysis of DTC clusters indicated that the average of 226 and 21 DTC clusters/subject were identified in metastatic and non-metastatic patients, respectively, and metastatic subjects showed 62% of DTC clusters EpCAM+, whereas 37% of clusters were EpCAM+ in non-metastatic patients. Comparing to the breast cancer serum biomarker CA15-3 detected in 32 metastatic cancer patients, showing positivity (≥28 ng/ml) of only 41% (13 out of 32), both CTCs (≥5) and DTCs (≥5) had a positivity rate of 81 (26 out of 32) and 97% (31 out of 32), respectively. Obtained results indicated that EpCAM+ CTCs and DTCs are reliable markers in terms of evaluating therapeutic efficacy and predicting cancer patients' prognosis.
Citation Format: Peter P. Lin, Junjian Li, Daisy Wang, Olivier Gires, Hongxia Wang. EpCAM differentially expressed on circulating and disseminated tumor cells promotes tumor metastasis in breast cancer 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 1059.
Abstract 1255: Delta-tocopherol induced endoplasmic reticulum stress causes autophagic degradation of ER and cell death in bladder cancer models
Authors: Blair Christopher A. , Hu Hanze , Huynh Tim , Wu Maggie , Yang Chung S. , Zi Xiaolin 
Published: August 2018

Abstract
Vitamin E has been the subject of numerous basic and clinical studies, which have demonstrated a range of results that necessitate the further analysis of its individual components. We demonstrate that of the major tocopherol components of Vitamin E, Delta tocopherol (δ-T) is significantly more effective than the more common Alpha- and Gamma- tocopherols at inducing bladder cancer cell death in vitro and reduces tumor growth and burden in vivo. As a major site of protein synthesis and folding the endoplasmic reticulum (ER) is highly sensitive to stress induced by increased unfolded protein load, which induces both pro-survival and ultimately pro-apoptotic responses via the different branches of the unfolded protein response (UPR). δ-T induces the UPR in human bladder cancer cells and ultimately results in cell death, inducing both apoptosis and autophagic cell death. Analysis of bladder cancer cells treated with δ-T revealed strong evidence of UPR activation in the form of upregulation and activation of ER stress sensors PERK and IRE1α, and the upregulation of folding chaperone GRP78 and transcription factors ATF4 and CHOP. These changes in turn induced downstream effects including Death Receptor 5 (DR5)-mediated apoptosis and visible induction of autophagy. In addition to the observation of autophagosome formation, induction of autophagy was further confirmed by upregulation of protein expression of components of the autophagic machinery LC3B and Atg family members. Electron Microscope imaging of treated cells revealed the presence of ER-whorls within the large autophagosomes which were themselves visible under conventional light microscopy, which has to our knowledge not been previously observed in cancer models. This observation is supported by the ER stress-based mechanism of action exhibited by δ-T on bladder cancer cells, which recapitulates the observations of the few previous reports of “ER-phagy” described in yeast models. ER stress induced expansion of the ER is believed to aid in the improvement of stressed cells' protein folding capacity, and selective degradation of the ER-whorls formed in this manner by a previously undescribed mechanism of autophagy was first described in yeast and remains unexplored in human cancer models. These findings may provide new insights into δ-T's mechanism of action and inform new approaches to the development of tocopherols as novel chemopreventive agents.
Citation Format: Christopher A. Blair, Hanze Hu, Tim Huynh, Maggie Wu, Chung S. Yang, Xiaolin Zi. Delta-tocopherol induced endoplasmic reticulum stress causes autophagic degradation of ER and cell death in bladder cancer models [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 1255.
Abstract 1427: Comprehensive investigation of false mutation discoveries in FFPE samples
Authors: Blomquist Thomas M. , Xiao Wenming ,   Somatic Mutation Working Group of the SEQC2 Consortium
Published: August 2018

Abstract
Next generation sequencing (NGS) has emerged as a primary tool for “precision” medicine, especially in the rapidly evolving field of cancer care. However NGS-based somatic variant calling in a clinical oncology setting is susceptible to numerous sources of technical error impeding optimal patient management. One important source of error in variant reporting is formalin fixation and paraffin embedding (FFPE). Of note, FFPE-derived errors are commonly present at clinically actionable loci and can occur at allelic frequencies (5-65%) that meet treatment criteria. Compounding this problem, degree of FFPE error is highly susceptible to inter-specimen and inter-laboratory variations. In this context, static variant calling thresholds to control for “general FFPE-effect” are likely inadequate; resulting in both False-Negatives (ignoring true somatic variation) and False-Positives (reporting technical error as truth). Despite the importance of fresh tissue for molecular studies, routine tissue histology (derived from FFPE) continues to be the gold standard for cancer staging/grading. And, as emphasis on smaller sample sizes becomes the norm, routine histology will be prioritized in many scenarios. Thus, the need to understand how molecular testing performs in FFPE tissue is a driving imperative for optimal cancer care.
In this study, our aim was to develop and evaluate “best” quality control practices that would minimize False-Positive or -Negative somatic variant calling in FFPE specimens. Reference samples (paired breast carcinoma and “normal” lymphoblast cell-lines) from the FDA-led Sequencing Quality Control Phase II (SEQC2) consortium were used. These specimens were subjected to varying FFPE conditions (n=8) mimicking the pathology laboratory setting. For each condition, multiple replicates of whole genome and exome sequencing (WGS/WES) were performed with ~100X coverage across the entire human genome. Observed somatic variation frequencies for each genomic position for each FFPE condition were compared to ground truth and quality control measures derived from matched fresh materials using numerous statistical models.
Applying rigorous analytical strategies, we aim to identify genomic regions that serve as markers (internal control regions) for the full range of FFPE-effect, develop QC measures and statistics to define lower limit of detection for variant calling for each genomic position, and provide general guidance for the community on how to accurately report mutations in FFPE processed clinical cancer specimens.
Citation Format: Thomas M. Blomquist, Wenming Xiao, Somatic Mutation Working Group of the SEQC2 Consortium. Comprehensive investigation of false mutation discoveries in FFPE samples [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 1427.
Abstract 1488: Inter-individual variation in hTERT regulation pathway genes in normal bronchial epithelial cells
Authors: Zolondek Rose , Craig Daniel J. , Crawford Erin L. , Willey James C. 
Published: August 2018

Abstract
Background: Genome-wide association studies (GWAS) and candidate gene studies suggest that telomere maintenance genes participate in etiology of lung cancer, idiopathic pulmonary fibrosis, and COPD. Telomeres are nucleoprotein structures located at the end of chromosomes that are maintained by telomerase encoded by hTERT. Telomerase is active in cancers, has the ability to aid in rapid cell division, and is dysfunctional in chronic conditions induced by inflammation as such as diabetes, renal failure, and COPD. hTERT is a known downstream target of β-catenin and WNT signaling. However, little is known regarding expression levels of these genes in normal bronchial epithelial cells (NBEC). The purpose of this study is to investigate inter-individual variation in regulation of β-catenin and WNT in NBEC, and if present, identify variants in regulatory region of human telomerase reverse transcriptase (hTERT) that could be used as candidate biomarkers for lung cancer risk. Methods: NBEC specimens from subjects with COPD (n=5) or without COPD (n=9) were obtained by bronchoscopy brush under IRB approved protocol. β-catenin, and WNT4 were measured by competitive multiplex-RT-PCR. Results: Both β-catenin and WNT4 displayed significant inter-individual variation as measured by Intra-Class Correlation (ICC) analysis (β-catenin ICC = 0.47, 95% Confidence Interval (0.2, 0.55), p &lt; 0.05; WNT4 ICC = 0.60, 95% Confidence Interval (0.35, 0.85), p &lt; 0.05). In patients with COPD, WNT4 expression was significantly higher in current smokers compared to former smokers (p&lt;0.05). Conclusions: Inter-individual variation in NBEC expression of β-catenin and/or WNT4 was observed and it is reasonable to test the hypothesis that these genes and related pathway genes may contribute to variation in regulation of hTERT in NBEC and risk for lung cancer, COPD, and/or other lung diseases.
Citation Format: Rose Zolondek, Daniel J. Craig, Erin L. Crawford, James C. Willey. Inter-individual variation in hTERT regulation pathway genes in normal bronchial epithelial 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 1488.
Abstract 167: Targeting the NF-kappaB pathway with bardoxolone methyl to inhibit ovarian cancer spheroid formation
Authors: Ozaki Michelle K. , House Carrie D. , Mazan-Mamczarz Krystyna , Lal-Nag Madhu , Thomas Craig , Annunziata Christina M. 
Published: August 2018

Abstract
Over 70% of patients with advanced stage ovarian cancer relapse within 2 years, with long term overall survival being only 25%. Tumor-initiating cells (TICs) are thought to contribute to this high rate of recurrence as they can resist killing by platinum-based chemotherapy. In this study we sought to identify pathways unique to TICs and to disrupt these pathways in order to more effectively target this population of cells. We conducted an siRNA screen which identified NF-kappaB signaling as an important pathway in the maintenance of ovarian cancer cells grown in non-adherent spheroid cultures that mimic TICs. Downregulation of several known NF-kappaB target genes, including NXF1, RAC2, CDC42, BCL2L1 and SERPINB3, significantly decreased growth of TIC cultures but not the corresponding adherent cultures, thereby indicating that expression of these genes is necessary for growth in TIC cultures. These findings are consistent with previous studies which showed that higher NF-kappaB activity is linked with drug resistance in patients. In parallel, we conducted a drug screen to identify compounds that target TICs. One clear candidate was bardoxolone methyl, which has been shown to inhibit IKK, an upstream NF-kappaB signaling protein. We confirmed the results of the drug screen in a panel of ovarian cancer cell lines, showing that bardoxolone methyl decreased known TIC markers CD133 and ALDH by flow cytometry, and decreased NF-kappaB proteins by western blot. To further elucidate the mechanism of bardoxolone methyl on TICs we conducted an RNAi screen +/- bardoxolone methyl. Interestingly, the knockdown of genes including BRAF, MAP3K8, LMNA and SMAD6 acted in a synthetically lethal manner with bardoxolone methyl in the TICs. To begin translating to a clinically relevant model, we proceeded to test whether bardoxolone methyl could eliminate TICs that remained after treatment with platinum-based chemotherapy. We confirmed in vitro that bardoxolone methyl in combination with chemotherapy reduced TIC populations. Our ongoing studies will address whether this drug is effective in preventing relapse in vivo after chemotherapy treatment of ovarian cancer in mouse models.
Citation Format: Michelle K. Ozaki, Carrie D. House, Krystyna Mazan-Mamczarz, Madhu Lal-Nag, Craig Thomas, Christina M. Annunziata. Targeting the NF-kappaB pathway with bardoxolone methyl to inhibit ovarian cancer spheroid formation [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 167.
Abstract 1749: CXCR4 inhibition modulates tumor microenvironment and robustly inhibits growth of B16-OVA melanoma
Authors: Saxena Ruchi , Wang Yan , Mier James W. 
Published: August 2018

Abstract
Background: The chemokine receptor CXCR4 is expressed on a range of immune cells. Additionally, CXCR4 has been found to be overexpressed in a variety of cancers and promotes cancer cell proliferation and metastasis, possibly by activating prosurvival signals that render cancer cells resistant to immune attack. Blockade of immune inhibitory pathways is emerging as an important therapeutic approach for the treatment of cancer. In our previous studies, X4-136, a CXCR4 antagonist, alone and in combination with various immune checkpoint inhibitor,s exhibited potent antitumor activity in the B16-OVA murine melanoma model. We report here results from additional in vivo studies as well as in vitro mechanistic experiments to determine the impact of CXCR4 inhibition on tumor cell gene expression and on immune phenotypes within the tumor microenvironment.
Methods: B16-OVA cells were implanted into C57BL/6 mice. Seven days post implantation, mice were treated with X4-136, anti-PD-L1, or the combination for 16 days. At sacrifice, tumors were excised and flash frozen in liquid nitrogen for Western blot analysis or treated with collagenase for the analysis of subpopulations of T-cells by FACS. Gene expression was determined by PCR and protein expression was analyzed by Western blot.
Results: X4-136 alone demonstrated more robust activity than anti-PD-L1. The antitumor activity of the anti-PD-L1 was further enhanced in combination with X4-136. Analysis of infiltrating immune cells by flow cytometry showed that X4-136 alone or in combination led to an increase of CD8+ T cells as well as CD8 and perforin double-positive T cells. A trend of decrease in both immunosuppressive populations, Treg and MDSC, was observed. This combination also led to a decrease in the expression of HIF-2α and cyclin D1 in comparison to tumors from vehicle-treated mice by Western blot analysis, suggesting an antiproliferative effect. Additional analysis of impacted genes and pathways will also be presented.
Conclusion: X4-136 alone increased tumor-infiltrating CD8+ T-cells and exhibited potent antitumor activity in the B16-OVA murine melanoma model. The enhanced antitumor activity was observed when X4-136 was added to anti-PD-L1 treatment. The activities observed were associated with the improved CD8+ T cells to Treg cells ratio and with improved tumor microenvironment.
Citation Format: Ruchi Saxena, Yan Wang, James W. Mier. CXCR4 inhibition modulates tumor microenvironment and robustly inhibits growth of B16-OVA melanoma [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 1749.