tbuckley/cabot-search huggingface dataset:
Abstract LB-053: Next-generation sequencing of T-cell receptor-beta gene rearrangements reveals dramatic expansion of T-cell clonotypes after CART-EGFRvIII therapy for glioblastoma
Authors: Donald M. O'Rourke, Fang Chen, Zev A. Binder, Irina Kulikovskaya, Minnal Gupta, Jeffrey Finklestein, David E. Ambrose, MacLean P. Nasrallah, Carl H. June, Simon F. Lacey, J. Joseph Melenhorst
Journal: Cancer Research (2017)

Abstract We are interested in the T cell repertoire in glioblastoma (GBM) patients who have been administered peripherally infused CART-EGFRvIII adoptive T cell therapy for recurrent EGFRvIII-positive GBM. On neuropathologic evaluation following GBM tumor resection, we noticed that several subjects had a robust lymphocytic infiltrate in their tumors following CART-EGFRvIII infusion, which was out of proportion to the level of CART-EGFRvIII genomic sequences observed. We sought to quantify the T cell infiltrate in five subjects whose tumors were resected at different time points following CART infusion (days 6-104). In these five subjects, we analyzed the T cell clonotypic repertoire in the infusion product and in pre- and post-infusion brain tumor specimens by deep sequencing the T cell receptor (TCR) Vβ chain of tumor-infiltrating T cells. Data analysis was performed using ImmunoSeq and exported data were further examined using Graphpad Prism. The infusion products in these patients were highly polyclonal with no clones represented above 1%. We found that in all five of these subjects, the number and frequency of unique TCRVβ clonotypes increased by several thousand (~20-fold) in post-infusion GBM specimens, and only a small portion of these unique TCRs were shared with pre-existing tumor-infiltrating specific T cells (TILs). A consistent finding in these patients was that the clonotype compositional diversity of T cells in the tumor bed post-infusion was considerably larger than the pre-CART vs. infusion product sharing frequency. These data indicate there was a significant increase in the number and clonotypic diversity of tumor-infiltrating T cells following intravenous CART-EGFRvIII infusion, but only a small proportion appears to be derived from the infusion product. Collectively, these results show that CART infusion can trigger accumulation of TILs. Whether or not these TILs respond to GBM neoantigens remains to be investigated. Citation Format: Donald M. O'Rourke, Fang Chen, Zev A. Binder, Irina Kulikovskaya, Minnal Gupta, Jeffrey Finklestein, David E. Ambrose, MacLean P. Nasrallah, Carl H. June, Simon F. Lacey, J. Joseph Melenhorst. Next-generation sequencing of T-cell receptor-beta gene rearrangements reveals dramatic expansion of T-cell clonotypes after CART-EGFRvIII therapy for glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-053. doi:10.1158/1538-7445.AM2017-LB-053
Abstract 4984: BNip3 suppresses hepatocellular carcinoma (HCC) growth by limiting lipogenesis
Authors: Kay F. Macleod
Journal: Cancer Research (2017)

Abstract BNip3 is a mitochondrial protein that promotes the turnover of mitochondria at the autophagolysosome when nutrient supplies are low. BNip3-null livers exhibit lipid accumulation and develop a phenotype mimicking non-alcoholic steatohepatitis, a known precursor for development of hepatocellular carcinoma (HCC). Additionally, BNip3 is silenced in human HCC and other malignancies and this loss often correlates with more aggressive tumors and worse outcomes. However, the functional significance of BNIP3 loss for growth and progression of HCC has not been determined. We utilized the diethylnitrosamine (DEN)-induced mouse model of HCC to determine how loss of BNip3 affected HCC development in the mouse. Wild type and BNip3-null mice were treated with DEN, and tumor burden (size and number) was assessed at 6, 8, and 10 months of age. We also generated primary HCC cell lines from the tumors arising in BNip3-null mice for in vitro analysis of tumor cell growth and metabolism. We observed that BNip3-null mice had reduced tumor latency and enhanced tumor growth rate in the liver following DEN treatment compared to wild type mice consistent with BNip3 functioning as a tumor suppressor of HCC. Interestingly, tumors arising in BNip3-null mice accumulated increased lipid and qPCR analysis of primary tumors and cell lines revealed increased expression of lipogenesis genes compared to wild type. Treatment with a novel fatty acid synthase inhibitor or re-expression of BNip3 in the BNip3-null HCC cell lines reduced tumor cell growth and lipogenesis, and promoted oxidative metabolism. These results indicate that BNip3 acts as a tumor suppressor in HCC by limiting de novo lipogenesis and suggest that fatty acid synthase inhibitors could be effective therapeutically against BNIP3 deficient HCC in patients. Citation Format: Kay F. Macleod. BNip3 suppresses hepatocellular carcinoma (HCC) growth by limiting lipogenesis [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 4984. doi:10.1158/1538-7445.AM2017-4984
the Safety and Efficacy of Deferasirox for the Transplant Patients with Iron Overload
Authors: Takayoshi Tachibana, Junya Kanda, Shinichiro Machida, Takeshi Saitou, Masatsugu Tanaka, Yuho Najima, Satoshi Koyama, Takuya Miyazaki, Eri Yamamoto, Masahiro Takeuchi, Satoshi Morita, Yoshinobu Kanda, Heiwa Kanamori, Shinichiro Okamoto
Journal: Blood (2016)
Abstract 4949: Longitudinal monitoring of cell-free DNA in patients with small cell lung cancer reveals dynamic insights into treatment efficacy and disease relapse
Authors: Christine M. Lovly, Karinna Almodovar, Wade T. Iams, Catherine B. Meador, Sally York, Leora Horn, Christopher K. Raymond, Jennifer Hernandez, Lee P. Lim
Journal: Cancer Research (2017)

Abstract Introduction: Small cell lung cancer (SCLC) is a highly lethal neuroendocrine malignancy that accounts for approximately 10-15% of all lung cancers and is responsible for approximately 30,000 deaths annually in the United States and 200,000 deaths worldwide every year1. There is an urgent need to develop novel treatment strategies for patients with this disease. We sought to improve the quality of patient care by establishing a liquid biopsy assay for rapid, noninvasive monitoring of disease burden. Design: The SCLC assay relies on targeted next-generation DNA sequencing of cell-free DNA (cfDNA) collected from patient plasma. The assay targets a panel of 14 genes that are frequently mutated in SCLC2. We examined a total of 141 plasma samples from a cohort of 27 patients. 11 patients had limited stage SCLC and 16 patients had extensive stage SCLC. The analyzed plasma samples were collected during the course of patient treatment and included time points before and after chemotherapy or immunotherapy. Results: We detected somatic, disease-associated mutations in the cfDNA of 78% of patient samples (21/27). The allele frequency of cfDNA ranged from ≤0.5% to ≥85%. The most commonly mutated genes were TP53 and RB1, which were found in 17/27 and 10/27 samples, respectively. We also detected single nucleotide variants in PIK3CA (3/27) and PTEN (1/27) as well as copy number variants in MYC and MYCL1 (2/27). The observed mutant allele frequencies in longitudinal samples tracked closely with treatment responses. Strikingly, we found instances where the assay detected the reappearance of tumor-associated markers several weeks before clinical evidence of relapse was detected. Conclusions: cfDNA sequencing allows for improved monitoring of disease burden, depth of responses to treatment, and timely warning of disease relapse in patients with SCLC. References: 1. Society, A.C., Cancer Facts and Figures 2015. American Cancer Society, Atlanta, Ga, 2015. 2. George, J. et al., Comprehensive genomic profiles of small cell lung cancer, Nature 524:47 Citation Format: Christine M. Lovly, Karinna Almodovar, Wade T. Iams, Catherine B. Meador, Sally York, Leora Horn, Christopher K. Raymond, Jennifer Hernandez, Lee P. Lim. Longitudinal monitoring of cell-free DNA in patients with small cell lung cancer reveals dynamic insights into treatment efficacy and disease relapse [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 4949. doi:10.1158/1538-7445.AM2017-4949
Abstract 4309: Mode of action of LTX315-induced cell death
Authors: HENG ZHOU, Allan Sauvat, Sylvère Durand, Sabrina Forveille, Takahiro Yamazaki, Sylvie Souquere, Valentina Sica, Øystein Rekdal, Oliver Kepp, Guido Kroemer
Journal: Cancer Research (2017)

Abstract The experimental anticancer agent LTX-315 is an amphipathic cationic peptide that efficiently eradicates cancer cells in vitro and in vivo. Attracted by its efficacy we launched an in depth mechanistic study on LTX-315. First we focused on the mode of action of LTX-315 and found that the agent failed to induce morphological signs of apoptosis but evoked necrotic phenotypes. Accordingly, LTX-315 failed to stimulate the activation of caspases, and the pan-caspase inhibitor Z-VAD-fmk was unable to reduce cell killing. We then studied its subcellular localization by fractionation of LTX-315-treated cells, and revealed that the agent was enriched in mitochondria and caused an immediate arrest of mitochondrial respiration without any major uncoupling effect. LTX-315 disrupted the mitochondrial network, dissipated the mitochondrial inner transmembrane potential, and caused the release of mitochondrial intermembrane proteins into the cytosol. Cells lacking the two pro-death multidomain proteins BAX and BAK, were less susceptible to LTX-315-mediated killing. Moreover, cells engineered to lose their mitochondria were resistant against LTX-315, underscoring the importance of this organelle for LTX-315-mediated cytotoxicity. Further, we observed that LTX-315 induced all known characteristics of immunogenic cell death, including calreticulin exposure, ATP secretion, HMGB1 exodus and type-1 interferon induction. When injected into established cancers, LTX-315 caused a transiently hemorrhagic focal necrosis that was accompanied by massive release of HMGB1 (from close-to-all cancer cells), as well caspase-3 activation in a fraction of the cells. Collectively, these results support the idea that LTX-315 triggers unregulated necrosis, and kills cancer cells by virtue of its capacity to permeabilize mitochondrial membranes. In addition, LTX-315 can induce ICD, hence explaining its capacity to mediate immune-dependent therapeutic effects. Citation Format: HENG ZHOU, Allan Sauvat, Sylvère Durand, Sabrina Forveille, Takahiro Yamazaki, Sylvie Souquere, Valentina Sica, Øystein Rekdal, Oliver Kepp, Guido Kroemer. Mode of action of LTX315-induced cell death [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 4309. doi:10.1158/1538-7445.AM2017-4309
Relationships between vascular/plasma biopterins and endothelial nitric oxide synthase coupling, endothelial function and inflammation, in human atherosclerosis
Authors: C A Antoniades, C Shirodaria, P Leeson, M Crabtree, R Pillai, C Ratnatunga, D Tousoulis, A Antonopoulos, C Stetanadis, K M Channon
Journal: Journal of the American College of Cardiology (2008)
Abstract 4651: Multiple platform evaluation of KRAS codon 12/13 reference material
Authors: Russell Garlick, Yves Konigshofer, Farol L. Tomson, Dale Yuzuki, Bharathi Anekella
Journal: Cancer Research (2017)

Abstract An assay’s ability to detect the presence of a KRAS driver mutation is critical when attempting to determine whether a tumor may respond to anti-EGFR therapy. Currently, there are two FDA approved companion diagnostics that can be used to assess whether there are mutations in KRAS codons 12 and 13, and both include their own internal controls. However, there is a need for external reference materials that allow laboratories to validate such assays - especially, at levels near their limits of detection (LODs). We describe the design of the Seraseq™ FFPE Tumor KRAS Reference Material. This reference material is composed of 7 different 5-micron FFPE curls that contain the 7 different KRAS mutations detected by the companion diagnostics: G12A, G12C, G12D, G12R, G12S, G12V and G13D. Each curl contains a mixture of KRAS wildtype GM24385 cells and a KRAS mutant cell line in sufficient quantity for most assays. KRAS mutant frequencies of about 5% were targeted and subsequently verified by digital PCR. A 5% mutant frequency was selected because it is near the LOD for the existing companion diagnostics, and is close to the minimum reported frequency of many next generation sequencing (NGS)-based assays that test for somatic variants. The reference material was evaluated using different methods, which include digital PCR, the Roche cobas® KRAS Mutation Test, the QIAGEN therascreen® KRAS RGQ PCR Kit and several NGS-based assays. Testing revealed general compatibility with these assays in that sufficient DNA could be extracted, and concordance of the results with the expected calls was high. For example, apparent DNA yields by Nanodrop with the cobas assay exceeded the required amount by more than 3-fold and all 7 curls led to a “mutation detected” result in duplicate testing. Interestingly, not all variants were detected with the therascreen assay, which may be due to some variants being present at slightly below the claimed LODs, however DNA yields were sufficient and the correct variants were identified. Finally, variant frequencies obtained by NGS were consistent with those observed by digital PCR. We conclude that the Seraseq FFPE Tumor KRAS Reference Material may be useful as part of KRAS codon 12/13 assay validation. Citation Format: Russell Garlick, Yves Konigshofer, Farol L. Tomson, Dale Yuzuki, Bharathi Anekella. Multiple platform evaluation of KRAS codon 12/13 reference material [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 4651. doi:10.1158/1538-7445.AM2017-4651
Abstract LB-278: Whole exome sequencing of metaplastic breast carcinoma indicates monoclonality with associated ductal carcinoma component
Authors: Bracha E. Avigdor, Katie Beierl, Christopher D. Gocke, Daniel J. Zabransky, Karen Cravero, Kelly Kyker-Snowmana, Berry Button, David Chu, Sarah Croessmann, Rory L. Cochran, Roisin M. Connolly, Ben H. Park, Ashley Cimino-Mathews, Sarah J. Wheelan
Journal: Cancer Research (2017)

Abstract Although most human cancers display a single histology, there are unusual cases where two or more distinct tissue types present within a primary tumor. One such example is metaplastic breast carcinoma. Metaplastic breast carcinoma is a rare but aggressive cancer with a heterogenous histology, including squamous, chondroid, and spindle cells. Metaplastic carcinomas often contain an admixed conventional ductal invasive or in situ mammary carcinoma component, and are typically triple-negative for estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 (HER-2) amplification/overexpression. An unanswered question is the origin of metaplastic breast cancers. While they may arise independently from their ductal components, their close juxtaposition favors a model that postulates a shared origin, either as two derivatives from the same primary cancer, or one histology as a clonal outgrowth of the other. Understanding the mechanism of development of these tumors may inform clinical decisions. We performed exome sequencing for paired metaplastic and adjacent conventional invasive ductal carcinomas in eight patients and created a pipeline to identify somatic variants and predict their functional impact in these samples, without having matched normal tissue. We then determined the genetic relationships between the histologically distinct compartments. In each case, the tumor components have nearly identical landscapes of somatic variation, implying that the differing histologies do not derive from genetic clonal divergence, suggesting that epigenetic or noncoding changes mediate the metaplastic phenotype. This indicates that alternative therapeutic approaches, including epigenetic therapies, may render metaplastic breast cancers susceptible to current and future therapies. Citation Format: Bracha E. Avigdor, Katie Beierl, Christopher D. Gocke, Daniel J. Zabransky, Karen Cravero, Kelly Kyker-Snowmana, Berry Button, David Chu, Sarah Croessmann, Rory L. Cochran, Roisin M. Connolly, Ben H. Park, Ashley Cimino-Mathews, Sarah J. Wheelan. Whole exome sequencing of metaplastic breast carcinoma indicates monoclonality with associated ductal carcinoma component [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-278. doi:10.1158/1538-7445.AM2017-LB-278
Abstract 4354: Methylation-mediated silenced <i>PYCARD</i> plays a key role in human prostate cancer
Authors: Shinichi Fukushige, Toshiya Miyauchi, Teppei Okubo, Koji Mitsuzuka, Yoichi Arai, Akira Horii
Journal: Cancer Research (2017)

Abstract Epigenetic gene silencing by aberrant DNA methylation leads to loss of key cellular pathways in tumorigenesis. In order to analyze effects of DNA methylation in prostate cancer, we constructed LNCaP-derived human prostate cancer cells that can induce global reactivation of hypermethylated genes by the methyl-CpG targeted transcriptional activation (MeTA) method. In MeTA, a cassette construct of MBD2-derived methyl-CpG binding domain (MBD) with NFκB-derived transcriptional activation domain is transfected into cancer cells. Then expressed MBD domain specifically binds to the hypermethylated promoter regions, and NFκB transcriptional activation domain recruits p300/CREB-binding protein (CBP) and reactivates hypermethylation-mediated silenced genes. A cell proliferation assay indicated that MeTA suppressed the growth of LNCaP cells. Furthermore, both flow cytometry and TUNEL assays demonstrated that MeTA induced apoptosis. In order to search genes responsible for apoptosis, we performed gene expression microarray analysis of MeTA-uninduced and -induced LNCaP cells: Five genes encoding apoptosis-inducing factors upregulated two-fold or more in accordance with the induction of MeTA; PYCARD (PYD and CARD domain containing), TNFRSF25 (tumor necrosis factor receptor superfamily 25), HRK (harakiri, BCL2 interacting protein), BIK (BCL2 interacting killer), and CIDEA (cell death-inducing DFFA-like effector a). These genes also contained CpG islands (CGIs) within ± 1,000-bp of the transcription start site. We focused on PYCARD and TNFRSF25 because these two genes upregulated 10-fold or more in accordance with the induction of MeTA. We found that both genes were hypermethylated and showed low expression levels in LNCaP prostate cancer cells, whereas only PYCARD was unmethylated in RWPE-1 normal prostate epithelial cells. We further analyzed primary prostate cancer tissues and found tumor-specific promoter hypermethylation of PYCARD in 53.8% (7/13; P &amp;lt; 0.01). These results suggest that methylation-mediated silencing of PYCARD contributes to escape from apoptosis in human prostate cancer, and MeTA may provide important clues to analyze changes in cancer cell phenotypes by DNA methylation alterations. Citation Format: Shinichi Fukushige, Toshiya Miyauchi, Teppei Okubo, Koji Mitsuzuka, Yoichi Arai, Akira Horii. Methylation-mediated silenced PYCARD plays a key role in human prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4354. doi:10.1158/1538-7445.AM2017-4354
Abstract 5340: Retrovirus insertion induces syncytin mediated exosomes delivery in prostate cancer cells
Authors: Berna Uygur, Leonid Chernomordik
Journal: Cancer Research (2017)

Abstract Activation of retroviruses in normal cells can induce tumors and a wide array of cancers contains retrovirus-like particles. The potential role of these endogenous retroviruses in the development and progression of tumors has been discussed in many studies. However the effects of retrovirus insertion into cancer cells have not yet been fully examined. In this study, we explore genetic material transfer either between retrovirus-transduced prostate cancer PC3 cells or between PC3 cells and their host environment through extracellular vesicles (EV) and virus-like particles. For these purposes, we transduced PC3 cells with either GFP-encoding retrovirus or with m-cherry-encoding lentivirus. Co-incubation of GFP-expressing cells with m-cherry-expressing cells for 72h yielded yellow PC3 cells. Yellow cells were also observed in the experiments where lentiviral m-cherry expressing PC3 cells were cultured with tissue culture medium from retrovirus GFP expressing PC3 cells. These results indicated that horizontal genetic information transfer involves neither fusion nor contact between the cells. Since incubation of the retrovirus GFP-expressing PC3 cells with the medium from the lentivirus m-cherry expressing PC3 cells, did not yield yellow cells the genetic material transfer requires retrovirus insertion in PC3 cells. Using Western blot and Q-PCR, we found the exosomes from the medium generated by retrovirus GFP expressing PC3 cells to carry human endogenous retroviral proteins syncytin 1 and 2 and contain RNAs encoding these proteins. Exosomes from the lentivirus m-cherry expressing PC3 cells had lower protein expression of Syncytin 1&amp;2 than exosomes from retrovirus GFP expressing PC3 cells. Application of Syncytin 1 or 2 antibodies to the medium generated by or co-cultured retrovirus GFP expressing PC3 and lentivirus m-cherry expressing PC3 cells suppressed horizontal transfer of the genetic information from retrovirus GFP expressing PC3 cells to other cells. The specific mechanisms by which retroviral transduction and syncytins control the generation of a GFP-encoding pseudotyped retrovirus or EV and the delivery of their content, as well as the role of the virus/EV-mediated horizontal genetic material transfer between prostate cancer cells and between prostate cancer and their microenvironment remain to be clarified. Citation Format: Berna Uygur, Leonid Chernomordik. Retrovirus insertion induces syncytin mediated exosomes delivery in prostate cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5340. doi:10.1158/1538-7445.AM2017-5340
Angus Osborn Robson
Authors: Marguerite Ferguson, Tony Hoare, Andrew Robson, John Wilkinson
Journal: BMJ (2017)

Angus Osborn Robson was proud to have been a general physician specialising in chest medicine during what he viewed as the heyday of the NHS. He was one of a close knit group of consultants based at Wycombe and Amersham hospitals, who developed excellent local services for patients and inspired a generation of junior doctors who were fortunate enough to be trained in such an exciting and dynamic district general hospital environment.

After his education at Haileybury School, he was encouraged into medicine by his uncle and mentor, Sir Kenneth Robson, who served as registrar of the Royal College of Physicians and with whom he shared an interest in chest medicine. Like Sir Kenneth, Angus qualified from the Middlesex Hospital Medical School, for which he developed a great loyalty and fondness. He met his future wife, Janet, who was nursing there; his eldest son qualified from the Middlesex in medicine, and his daughter qualified as a physiotherapist there. Both sons were born at the Middlesex.

Angus did national service in the Royal Air Force’s …