tbuckley/cabot-search huggingface dataset:
Abstract 4980: Engineering adoptive T cell therapy for efficacy in ovarian cancer
Authors: Kristin G. Anderson, Breanna M. Bates, Edison Y. Chiu, Philip D. Greenberg
Journal: Cancer Research (2017)

Abstract Over 20,000 women are diagnosed with ovarian cancer annually - more than half will die within 5 years and this rate has changed very little in the last 20 years, highlighting the need for innovative therapies. One promising new treatment strategy has the potential to control tumor growth without toxicity to healthy tissues, by employing immune T cells engineered to target proteins uniquely overexpressed in tumors. Recent technological advances have helped identify and validate Wilms’ Tumor Antigen 1 (WT1) and mesothelin (MSLN) as valid antigen targets for ovarian cancer, as these proteins contribute to malignant and invasive phenotypes and have limited expression in healthy cells. In preclinical studies using either patient-derived cell lines or the mouse ID8 ovarian tumor model, we found that T cells engineered to express either a WT1- or MSLN- specific high-affinity T cell receptor (TCR) can kill human and murine ovarian tumor cells in vitro. Moreover, in a disseminated in vivo murine model, adoptively transferred TCR-engineered T cells preferentially accumulated within established ID8 tumors, delayed ovarian tumor growth and prolonged mouse survival. However, our data also revealed that the tumor microenvironment (TME) can limit engineered T cell persistence and killing capacity. Cellular and molecular analyses showed human therapy will face similar TME-mediated obstacles. The ovarian cancer TME is a nutrient- and oxygen-deprived milieu, and adaptive metabolic responses by infiltrating T cells have protean effects on T cell function. Thus, strategies that modulate T cell metabolic pathways, and thereby influence activity in the TME, might enhance T cell function and improve anti-tumor efficacy by overcoming a critical component of immune evasion by solid tumors. Ongoing studies will be discussed that are exploring strategies to overcome elements common to the human and murine TME, including direct modulation of the environment and T cell engineering to promote T cell survival and function. Citation Format: Kristin G. Anderson, Breanna M. Bates, Edison Y. Chiu, Philip D. Greenberg. Engineering adoptive T cell therapy for efficacy in ovarian 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 4980. doi:10.1158/1538-7445.AM2017-4980
Abstract 516: High-throughput functional evaluation of variants of unknown significance inEGFR
Authors: Shinji Kohsaka, Masaaki Nagano, Toshihide Ueno, Yoshiyuki Suehara, Takuo Hayashi, Naoko Shimada, Kazuhisa Takahashi, Kenji Suzuki, Kazuya Takamochi, Fumiyuki Takahashi, Hiroyuki Mano
Journal: Cancer Research (2017)

Abstract Since transforming mutations in epidermal growth factor receptor gene (EGFR) were first identified in non-small-cell lung carcinoma (NSCLC), advancement of diagnostics for such mutations, and evolution of targeted therapeutics against EGFR has driven unprecedented improvements in the management as well as outcome of patients with this lethal disease. However, next-generation sequencer (NGS)-driven extensive analyses on NSCLC have revealed a large number of variants of uncertain significance (VUS) in EGFR and other regions in the cancer genome that await further investigation. Here we present a mixed all nominated mutants in one (MANO) method to evaluate the transforming potential and drug sensitivity of VUS of oncogenes, and applied this method to 101 non-synonymous EGFR mutants in a high-throughput manner. The sensitivity of individual mutants to tyrosine kinase inhibitors (TKIs) against EGFR was shown diverged, ranging from relatively insensitive mutations such as missense mutations within exon 19 to a highly resistant mutation within exon 21. Our data thus support the importance of examining uncommon mutations within EGFR, and also of functional evaluation of such mutations. Our MANO method may become a novel foundation for in vitro and in vivo assessments of variants of cancer-related genes to deliver precision medicine to individual cancer patients. Citation Format: Shinji Kohsaka, Masaaki Nagano, Toshihide Ueno, Yoshiyuki Suehara, Takuo Hayashi, Naoko Shimada, Kazuhisa Takahashi, Kenji Suzuki, Kazuya Takamochi, Fumiyuki Takahashi, Hiroyuki Mano. High-throughput functional evaluation of variants of unknown significance in EGFR [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 516. doi:10.1158/1538-7445.AM2017-516
Abstract 5390: Broad Genomics and Cancer Program development of comprehensive blood biopsy sequencing capabilities to support direct-to-patient cancer research initiatives
Authors: Carrie Cibulskis, Andrew Hollinger
Journal: Cancer Research (2017)

Abstract Genomic profiling of cell free tumor DNA (Blood Biopsy) offers the potential to revolutionize cancer precision medicine. As a proxy for tumor tissue profiling, successful blood biopsy analysis can help select appropriate patients for clinical trials, provide useful data for treatment monitoring, and discover genomic mechanisms of disease resistance. Recognizing these potential benefits, we aim to enable large-scale genomic data generation and analysis of cfDNA samples to support the patient driven Metastatic Breast Cancer Project (mbcproject.org) and many other such efforts. The widespread adoption of cfDNA sequencing technology in clinical research will require low cost, efficient, and in some cases clinically-validated processes. Commercial offerings in this field are focused on analysis of small targeted hotspot panels due to the challenges of more complete sequencing approaches for cfDNA (e.g. variability in the fraction of tumor present and high false positive rates). Working in collaboration with the Broad Institute Cancer Program, we have developed a process to overcome these challenges and provide high quality comprehensive exome analysis of cfDNA. Our process includes screening samples using ultra low pass, UMI-enabled whole genome sequencing to quantify the % of tumor DNA available for sequencing. Qualified samples are then moved into automated processes for exome sequencing and somatic mutation detection. In our initial validation study of 23 breast and prostate cancer patients with matched cfDNA and tumor tissue sequencing, we are able to identify 90% of clonal and 45% of subclonal mutations found in the matched tumor biopsy. In our effort to scale this process, and fully characterize the benefits and limitations of this technology we will present additional validation analysis. We will evaluate the relative importance of using paired sample analysis (tumors and matched normals) with analysis of tumor sequencing alone and assess sensitivity and specificity of somatic alterations as a function of tumor fraction and sequencing depth. Citation Format: Carrie Cibulskis, Andrew Hollinger. Broad Genomics and Cancer Program development of comprehensive blood biopsy sequencing capabilities to support direct-to-patient cancer research initiatives [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 5390. doi:10.1158/1538-7445.AM2017-5390
Abstract 58: Local intratumoral treatment with anti-mesothelin Immunotoxins overcomes resistance to anti-CTLA-4 therapy
Authors: Yasmin Leshem, Xiu-fen Liu, Tapan Bera, Masaki Terabe, Jay A. Berzofsky, Birgit Bossenmaier, Gerhard Niederfellner, James O'Brien, Yoram Reiter, Ira Pastan
Journal: Cancer Research (2017)

Abstract Background: SS1P and RG7787 are immunotoxins composed of anti-mesothelin antibody fused to a fragment from pseudomonas exotoxin A. We previously observed delayed tumor responses in patients treated with SS1P leading us to hypothesis that immunotoxins can provoke anti-tumor immunity. We hypothesize that intra-tumoral injection of SS1P or RG7787 will produce immunologic death and convert living tumors to a source of antigens and boost the therapeutic effect of immune check point blockade. Method: A BALB/c breast cancer cell line was transfected with human mesothelin (66C14-M) and grown in BALB/c mice transgenic for human mesothelin. SS1P or RG7787 was injected directly into established tumors (80-100 mm3) and anti-CTLA-4 administered IP. Results: We observed total tumor regressions in 23 out of 38 mice (60%) treated with anti-CTLA-4 and either RG7787 or SS1P. No cure was achieved when the drugs were given as a monotherapy supporting the case for synergic anti-tumor activity. Pathologic evaluation of regressing tumors showed a massive inflammation of admixed eosinophils and mononuclear cells located in a collar surrounding the tumors. Tumor regression was associated with increased number of CD8+ cells and was blocked when CD8+ cells were depleted by an antibody. In addition, cured mice were resistant to re-implantation of 66C14 cells not expressing mesothelin indicating that a long-term anti-tumor immunity was formed. To determine if pathogen associated molecular patterns contributed to the response, we combined anti-CTLA-4 with an inactive RG7787 and observed a major reduction in anti-tumor activity (P&amp;lt;0.01) indicating that the effect is not mediated by recognition of a foreign bacterial protein. Conclusions: We suggest that injecting immunotoxins into tumors is a useful approach to boost the activity of anti-CTLA-4. Based on the synergistic anti-tumor effect demonstrated in this study we believe that there is a strong rational to explore such combination therapies in patients. Citation Format: Yasmin Leshem, Xiu-fen Liu, Tapan Bera, Masaki Terabe, Jay A. Berzofsky, Birgit Bossenmaier, Gerhard Niederfellner, James O'Brien, Yoram Reiter, Ira Pastan. Local intratumoral treatment with anti-mesothelin Immunotoxins overcomes resistance to anti-CTLA-4 therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 58. doi:10.1158/1538-7445.AM2017-58
Abstract 4623: Transcriptional analysis of the functional differences between M1 and M2 macrophages to identify new targets for myeloid cell modulation in pancreatic tumors
Authors: Kimberline R. Yang, Todd D. Armstrong, Elizabeth M. Jaffee
Journal: Cancer Research (2017)

Abstract Macrophages exhibit dynamic plasticity in their function in response to the accumulating genetic alterations that occur during tumorigenesis, resulting in the establishment of an immune tolerized tumor microenvironment. However, depending on their environmental cues, they can switch between two functional phenotypes: pro-inflammatory/anti-tumorigenic (M1) or anti-inflammatory/pro-tumorigenic (M2). The importance of these two macrophage subsets is well-recognized; however, identifying and distinguishing M1 from M2 macrophages in patient tumors still remains a challenge. Prior studies have utilized transcriptome profiling of artificially skewed M1 and M2 macrophages from healthy donors to identify individual genes or gene clusters unique to each macrophage subset. However, these studies are limited to surface marker expression and gene expression profiles alone to distinguish subsets and lack functional validation of M1 and M2 macrophages. Surface marker and gene expression profiling of human M1 and M2 macrophages provide an incomplete characterization, as functionality is an important feature distinguishing these macrophage subsets. To improve the characterization of M1 and M2 macrophages, we performed a thorough three-step validation of artificially skewed M1 and M2 macrophages from healthy donor monocytes using surface marker expression, gene expression profiling, and multi-analyte ELISA analyses. Using our validation assays, we tested previously published protocols for their efficacy in generating M1 and M2 macrophages. While M1 macrophages using these protocols generated as expected M1 characteristics, M2 macrophages lacked hallmark functional features, particularly IL-10 secretion. This necessitated the generation of an optimized protocol to skew M1 and M2 macrophages that exhibited distinctive surface marker expression, gene expression profiles, and cytokine and chemokine production for their respective subset. We then performed RNA-sequencing to interrogate the transcriptional landscape of functional M1 and M2 macrophages and have found 1,472 transcripts that have at least a two-fold change in differential expression between M1 and M2 macrophages across 4 different donors. These results represent the most in-depth characterization of human M1 and M2 macrophages and provide insights into better biomarkers and targets for novel immunotherapy approaches. Citation Format: Kimberline R. Yang, Todd D. Armstrong, Elizabeth M. Jaffee. Transcriptional analysis of the functional differences between M1 and M2 macrophages to identify new targets for myeloid cell modulation in pancreatic tumors [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 4623. doi:10.1158/1538-7445.AM2017-4623
Abstract 2744: Inter-site comparison of performance of an ultra-sensitive sequencing technology for circulating tumor DNA
Authors: Stephanie Yaung, Alex Lovejoy, Dan Klass, Fergal Casey, Aruna Arcot, Melissa Loyzer, William Chiu, Nabil Azhar, Sophie Beckert, Maria Lange, Sandra Siemann, Sebastian Froehler, Shelly Gunn, John F. Palma
Journal: Cancer Research (2017)

Abstract The combination of liquid biopsies and ultra-sensitive next-generation sequencing (NGS) holds tremendous promise in oncology for the detection and surveillance of somatic mutations that correlate with diagnosis, prognosis, response prediction, resistance monitoring and tumor burden. We have developed a capture-based NGS workflow that provides ultra-sensitive detection of 4 mutation classes - single nucleotide variants (SNVs), insertions/deletions, copy number amplifications (CNAs) and fusions - from low input cell-free DNA isolated from plasma. Sensitivity and specificity of 2 different AVENIO ctDNA Analysis Kits (for Research Use Only) across 3 sites for 48 samples that included contrived DNA blends with known mutations validated by digital PCR and normal reference plasma samples were assessed. The AVENIO ctDNA Targeted Kit (Targeted) was designed to detect mutations in 17 genes, across 80kb, included in NCCN Guidelines for solid tumors plus additional variants relevant for therapy selection. The AVENIO ctDNA Expanded Kit (Expanded) was designed to detect mutations in 77 genes, across 200kb, associated with solid tumor including variants relevant for clinical trial research. Testing sites achieved 100% sensitivity for SNVs and fusions at 0.5% and 1% allelic frequency, respectively, from 30 ng of input DNA for both kits. Median coverage of 4,200-6,400X was greater with the Targeted kit relative to that of 2,700-3,800X with the Expanded kit. Specificity was 100% for the Targeted kit either by sample or variant. The Expanded kit had a specificity of 91.7-100% by sample and 99.7-100% by variant. At an expected 5X or 8X copy number amplification for multiple genes, both the Targeted and Expanded kits were 100% sensitive and 93.1-98.4% specific per gene. The specificity for fusion detection was 100% for both kits down to 1% mutant allele frequency. The AVENIO ctDNA Analysis Kits for plasma and NGS applications provide exquisite sensitivity and specificity for the simultaneous detection of 4 different mutation classes. Citation Format: Stephanie Yaung, Alex Lovejoy, Dan Klass, Fergal Casey, Aruna Arcot, Melissa Loyzer, William Chiu, Nabil Azhar, Sophie Beckert, Maria Lange, Sandra Siemann, Sebastian Froehler, Shelly Gunn, John F. Palma. Inter-site comparison of performance of an ultra-sensitive sequencing technology for circulating tumor DNA [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 2744. doi:10.1158/1538-7445.AM2017-2744
Abstract LB-154: Methylation profiling of ovarian cancer shows prognostic heterogeneity of histological subtypes and high-grade serous
Authors: Clara Bodelon
Journal: Cancer Research (2017)

Abstract Background. Ovarian cancer is a heterogeneous disease that is divisible into multiple subtypes with variable pathogenesis, etiology and biological behavior. We analyzed DNA methylation profiling data to identify biologic subgroups of ovarian cancer and study their relationship with histologic subtypes and prognosis. Methods. A total of 176 paraffin embedded ovarian epithelial tumor tissues, including the four major epithelial ovarian tumor subtypes (serous, endometrioid, mucinous and clear cell) and tumors of low malignant potential (LMP) were selected from two different sources: The Polish Ovarian Cancer study, an incident population-based case-control study conducted from 2001-2004, and the Surveillance, Epidemiology, and End Results Residual Tissue Repository (SEER RTR), which included ovarian tumors blocks collected between 1994 and 2004 from the Iowa and Hawaii SEER registries. The distributions of tumor histologic subtypes and grades from the studies were similar. All analyses were restricted to Caucasian women. Methylation profiling was conducted using the Illumina 450K methylation array. Analyses were restricted to the 22 autosomal chromosomes and non-SNP probes. Fourteen samples that did not pass quality control were excluded from the analysis. Results. Among 162 samples, 32 were from the Polish study and 130 were from the SEER RTR. Unsupervised hierarchical clustering of the 5,000 most variable CpG sites showed 4 major clusters: Cluster 1 with 79% invasive serous and 14% endometrioid carcinomas, including the majority of high grade carcinomas; cluster 2 with 77% either endometrioid or clear cell carcinomas; cluster 3 with 71% serous LMP; and cluster 4 with 73% mucinous carcinomas. We observed significant survival differences across these clusters (long-rank test P= 4.27×10-6), similar to differences observed for histologic subtypes. Within high grade (HG) serous carcinomas, clustering showed three subgroups with prognostic significance (long-rank test P= 0.008). Conclusions. Our results suggest that methylation-based subtypes provide a classification of ovarian tumors that are in agreement with morphologic subtypes and probable mechanisms of origin. Unsupervised clustering analysis of HG serous carcinomas showed subtypes within HG serous with significance survival difference. Ongoing analyses are comparing performance of the methylation subgroups with gene expression subgroups of ovarian cancer. Citation Format: Clara Bodelon. Methylation profiling of ovarian cancer shows prognostic heterogeneity of histological subtypes and high-grade serous [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 LB-154. doi:10.1158/1538-7445.AM2017-LB-154
New treatment of Wilson´s disease
Authors: Miroslav Vetrik, Jana Mattova, Jan Kucka, Hana Mackova, Ondrej Sedlacek, Pavla Pouckova, Olivia Policianova, Jiri Brus, Sebastian Eigner, Ludek Sevc, Petr Stepanek, Martin Hruby
Journal: Journal of Controlled Release (2017)
Abstract 610: Blockade of tumor expression of PD-1 promotes lung cancer growth in a murine model
Authors: Shisuo Du, Qing Guan, Adam P. Dicker, Bo LU
Journal: Cancer Research (2017)

Abstract Lung cancer remains one of the most prevalent and fatal malignancies worldwide. There are substantial evidences that immunotherapies offer significant benefits among lung cancer patients. Pembrolizumab, a humanized programmed death receptor-1(anti-PD-1) antibody is now approved by FDA as a first-line treatment of patients with metastatic non-small cell lung cancer (NSCLC). Recent data demonstrate that PD-1 is not only expressed by immune cells, but also by human melanoma cells. However, little is known about the biological significance of PD-1 pathway in cancer including NSCLC. Thus, we examined PD-1 expression in a series of established murine lung cancer cell lines. RT-PCR amplification and sequencing of the full coding sequence of the murine PD-1 (PDCD1) gene revealed the presence of PDCD1 mRNA in the M109 lung cancer cells. Flow cytometry and immunofluorescence analysis demonstrated PD-1 protein expression in these murine lung cancer cells. To determine the molecular function of tumor PD-1 in lung cancer survival, we treated M109 cells in culture with either anti- mouse PD-1(100ug/ml) or isotype control antibody and found that PD-1 inhibition significantly enhanced cancer cell viability as measured by MTT and clonogenic assay. Alternative PD1 inhibition by either knockdown of PDCD1 via siRNA or knockout of PDCD1 by CRISPR-Cas9 all lead to increased survival of M109 cells. Furthermore, PDCD1-knockout M109 cells had no survival difference in the presence of anti-PD1 compared to its PD1-expressing parental cells. Conversely, treatment with recombinant PD-L1 fusion protein exhibited significantly increased apoptotic rates (7.5±3.2% vs 2.1±1.2%) suppressing the tumor cell growth in the wild-type M109 in culture. To validate these results in in vivo models, NSG mice were used to determine the direct impact of anti-PD1 on M109 xenografts without the interplay of host immune system. M109 xenografts treated with antiPD-1 (10mg/kg i.p.) antibodies showed accelerated growth compared to those treated by IgG control (2487±473 vs 1499±292mm3 at days 21 after tumor inoculation, p=0.013). M109 subcutaneous tumors in the PD-1 knockout mice also manifested more rapid growth than the same tumors implanted in wild-type mice. Taken together, our results uncover a novel function of PD-1/PD-L1 axis in lung cancer survival and implicate possible tumor-promoting effects from anti-PD-1 therapy upon PD1-expressing lung cancer in the absence of effective immune response. We plan to interrogate bio-specimens collected through NRG trials to establish the translational potential of these findings. Citation Format: Shisuo Du, Qing Guan, Adam P. Dicker, Bo LU. Blockade of tumor expression of PD-1 promotes lung cancer growth in a murine model [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 610. doi:10.1158/1538-7445.AM2017-610