bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3998: Sequencing the B-cell and T-cell repertoire
Authors: Stewart Fiona J. , Karaca Mehmet , Adams Kris , Clouser Chris , Patel Bonny , Timberlake Sonia , Donahue William , Apone Lynne , Russello Salvatore , Dimalanta Eileen T. , Davis Theodore B. , Vigneault Francois 
Published: July 2016

Abstract
Immune sequencing allows for the study of complex immunological diseases by sequencing millions of V(D)J combinations from B-cell antibody and T-cell receptors. The popularity of this technique has increased due to recent throughput and read length improvements in next-generation sequencing technologies. However, structural and sequence complexities of antibody genes have made reliable targeting approaches challenging.
We have developed and optimized a method for accurate sequencing of full-length immune gene repertoires of B-cells and T-cells. The method uses a unique barcoding scheme specifically designed to tag every mRNA molecule with a unique identifier (UID) so that all PCR copies of each mRNA fragment can be collapsed into a single consensus sequence. This makes the assay extremely accurate, by resolving PCR bias and sequencing errors as well as allowing quantitative digital molecule counting.
Immune sequencing libraries were generated from total RNA extracted from Peripheral Blood Mononuclear Cells in duplicate from a single patient. The use of UIDs enabled absolute quantification of starting RNA molecules present in the original sample and therefore accurate ranking of the antibody clone abundance, by avoiding the bias incorporated by PCR or sequencing when total reads only were measured. Using the same sequencing method, tumor samples were analyzed for abundance of expanded clones via grouping clones by V gene, J gene and CDR3 similarity and ranking by mRNA abundance. Additionally, the use of isotype-specific primers (IgM, IgD, IgG, IgA and IgE) enabled measurement of the heavy chain isotype proportions within the samples. Further, alignment of full-length heavy chain antibody sequences generated using this method to germline genes from reference databases enabled quantitation of the mutation level of each antibody sequence, thereby providing information on the overall maturity and mutational profile of the sample repertoire.
Citation Format: Fiona J. Stewart, Mehmet Karaca, Kris Adams, Chris Clouser, Bonny Patel, Sonia Timberlake, William Donahue, Lynne Apone, Salvatore Russello, Eileen T. Dimalanta, Theodore B. Davis, Francois Vigneault. Sequencing the B-cell and T-cell repertoire. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3998.
Abstract 3999: Altering the balance between immune activation versus regulation in the skin to promote CD8 T-cell activity within epithelial cancers
Authors: Bridge Jennifer A. , Overgaard Nana H. , Steptoe Raymond J. , Frazer Ian H. , Wells James W. 
Published: July 2016

Abstract
The Human Papilloma Virus (HPV) 16 is a high-risk HPV known to be a causative agent in numerous cancers including cervical cancer. While prophylactic vaccines exist to combat the spread of HPV16, successful therapeutic vaccines to combat established HPV16-associcated disease remain elusive. The expression, in a mouse model (“E7”), of the HPV16 E7 gene in keratinocytes under the control of the K14 promoter, leads to a local immune suppressive environment, as evidenced by the lack of graft rejection when E7 skin grafts are placed on WT recipient mice. Furthermore, well healed (&gt;30 days) E7 skin grafts are not rejected when mice are immunised with E7 peptide in combination with Quil A- or CASAC-based adjuvants. This is despite a substantial increase in E7 peptide/H-2Db pentamer staining in the blood, and marked killing of E7-peptide expressing TC-1 cells when injected i.v., confirming that CD8 T-cells respond to vaccination and differentiate into CTL capable of killing E7-expressing target cells. We hypothesised that the removal of regulatory T-cells (T-reg) might lead to E7 graft rejection in immunised mice. The co-administration of an anti-CD4-depeting antibody at the time of immunisation led to rejection of ∼50% of grafts. To confirm a role for T-reg, E7-grafted T-reg-deficient Rag1-/- mice received purified donor CD8 T-cells from E7-vaccinated WT mice. FACS staining of Rag1-/- lymph nodes 30 days post CD8+ T-cell transfer confirmed the absence of classical CD4+FoxP3+ Treg, however the E7 grafts did not reject. As in the WT mice however, rejection could be induced through the co-administration of an anti-CD4 antibody. The data suggest that the removal of a CD4+, non T-reg cell, leads to CD8+ T-cell activity in the skin as evidenced by E7 skin graft destruction.
Citation Format: Jennifer A. Bridge, Nana H. Overgaard, Raymond J. Steptoe, Ian H. Frazer, James W. Wells. Altering the balance between immune activation versus regulation in the skin to promote CD8 T-cell activity within epithelial cancers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3999.
Abstract 40: Metabolic rewiring in Rb deficient cells during cancer progression
Authors: Kohno Susumu , Okahashi Nobuyuki , Kitajima Shunsuke , Suzuki Sawako , Tanaka Tomoaki , Matsuda Fumio , Shimizu Hiroshi , Takahashi Chiaki 
Published: July 2016

Abstract
Tumor suppressors control critical steps of cellular metabolism and its inactivation induces cancer specific-metabolic features including aerobic glycolysis. Glycolysis contributes to energy generation and supplying precursors of biomass, e.g., nucleotide, amino sugar, amino acid and lipids. These macromolecules were required for proliferation and cancer survival. Although aerobic glycolysis is now widely accepted as a metabolic feature of cancer, its causal relationship with cancer progression is still unclear.
In common type cancers, inactivation of RB tumor suppressor is prevalently observed during tumor progression. Previous studies demonstrated RB inactivation induces inflammation, angiogenesis, drug resistance, etc., as well as cell cycle progression. We currently focus on the impact of RB deficiency on the central carbon metabolism, e.g., glycolysis, TCA cycle and glutamine metabolism. To address this point, we established a mouse model in which RB depletion in p53-null soft tissue sarcoma cells induced undifferentiated phenotype associated with “glycolytic to glutaminolytic” switch (metabolic rewiring) most probably due to down-regulation of Pgam2 activity. Up-regulation of Pgam2 in these cells antagonized the metabolic rewiring, and suppressed spherogenic and tumorigenic activities of RB deficient cells, however did not affect cell proliferation in 2D culture conditions. Moreover, Pgam2 depletion suppressed RB-dependent myogenic differentiation. These findings suggest that RB controls tumorigenicity and differentiation by influencing central carbon metabolism via Pgam2.
Citation Format: Susumu Kohno, Nobuyuki Okahashi, Shunsuke Kitajima, Sawako Suzuki, Tomoaki Tanaka, Fumio Matsuda, Hiroshi Shimizu, Chiaki Takahashi. Metabolic rewiring in Rb deficient cells during cancer progression. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 40.
Abstract 4031: Different expression of programmed death 1 (PD1) and its ligand (PD-L1) in esophageal and gastric cancer
Authors: Däster Silvio , Eppenberger-Castori Serenella , Droeser Raoul A. , Schaefer Hannah M. , Spagnoli Giulio C. , Terracciano Luigi , Tornillo Luigi , von Holzen Urs 
Published: July 2016

Abstract
Background: Prognosis of gastric and esophageal cancer remains poor. Improvements in gastric and esophageal cancer treatments are urgently needed. Programmed cell death 1 receptor (PD1) and its ligand 1 (PD-L1) are known to interact with T cells promoting epithelial cancer tolerance. Several therapeutic monoclonal antibodies blocking this interaction are reaching the clinical praxis. Therefore it is relevant to investigate the role of these biomarkers in different types of malignancy.
Methods: Four different copies of tissue microarrays (TMA), each including healthy mucosa (n = 74) and a total of 241 clinically annotated malignancies of the esophagus (n = 80) and stomach (n = 161) were constructed and stained with PD1, PD-L1, and CD8 specific reagents.
Results: Interestingly, only two cancer samples out of the 241 specimens investigated weakly expressed PD-L1. None of the normal mucosa epithelial cells expressed PD-L1. Stromal PD1 expression correlated with infiltration by CD8+ lymphocytes (rho = 0.4; P&lt;0.0001). Elevated intraepithelial presence of CD8+ and/or PD1+ cells in gastric cancer was significantly correlated with longer patients’ survival. No correlation could be found in esophageal cancer.
Conclusion: In contrast to other epithelial cancers, PD-L1 expression was virtually absent in the investigated malignancies of the esophagus and stomach. PD1 expression in the stroma surrounding such malignancies correlated with intraepithelial presence of T-cells CD8+ expression, and with better prognosis in gastric cancer patients.
Citation Format: Silvio Däster, Serenella Eppenberger-Castori, Raoul A. Droeser, Hannah M. Schaefer, Giulio C. Spagnoli, Luigi Terracciano, Luigi Tornillo, Urs von Holzen. Different expression of programmed death 1 (PD1) and its ligand (PD-L1) in esophageal and gastric cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4031.
Abstract 4037: Enhancement of efferocytosis by rhoA kinase inhibitor following doxorubicin treatment synergistically reduces tumor growth
Authors: Nam Gihoon , Kim In-San 
Published: July 2016

Abstract
Massive dying of tumor cells after chemotherapy may promote chronic inflammation which favors tumor growth by uncleared secondary necrotic cells. Given that defects in apoptotic cell clearance have been linked with various inflammatory diseases and autoimmunity, the prompt removal of apoptotic cells by phagocytes is important for anti-tumor immunity. To improve the anti-tumor effect of doxorubicin, we investigated the role of RhoA-kinase (ROCK) inhibitors on efferocytosis by macrophages, which is important for anti-tumor immunity and tissue regeneration. Treatment of bone marrow-derived macrophages (BMDMs) with ROCK inhibitor increased efferocytosis of dying tumor cells by doxorubicin in vitro. ROCK-blockade after doxorubicin treatment group showed effective inhibition of tumor growth and also T cell-mediated elimination of immunogenic tumors more than the doxorubicin monotherapy group in established tumor models. Furthermore, we also confirmed that macrophage depletion abrogated the therapeutic effect of ROCK inhibitor after doxorubicin treatment on tumor growth. Taken together, our findings indicate that ROCK inhibitor following doxorubicin treatment reduced tumor growth via efferocytosis enhancement.
Citation Format: Gihoon Nam, In-San Kim. Enhancement of efferocytosis by rhoA kinase inhibitor following doxorubicin treatment synergistically reduces tumor growth. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4037.
Abstract 4052: The role of the phosphorylated RXRα on diethylnitrosamine-induced liver tumorigenesis in mice
Authors: Sakai Hiroyasu , Shirakami Yohei , Shimizu Masahito 
Published: July 2016

Abstract
We have previously reported that a malfunction of RXRα due to aberrant phosphorylation at serine 260 by MAPK is associated with the development of hepatocellular carcinoma (HCC). The phosphorylated RXRα impairs normal receptor functions of either RXR or RAR, which are respective homodimeric or heterodimeric partner of RXRα, in a dominant-negative manner. Besides, these impaired receptor functions result in the downregulation of their target gene expression and inducing hepatocarcinogenesis by stimulating cell proliferation and inhibiting apoptosis, suggesting that phosphorylated RXRα plays a crucial role in the development of HCC. However, these findings were revealed primarily using HCC cell lines that express the phosphorylated-RXRα (p-RXRα) proteins and it still remains unclear whether p-RXRα may impact in the process of hepatocarcinogenesis in vivo. Therefore, in order to investigate the biological functions of p-RXRα on hepatocarcinogenesis in vivo, we generated doxycycline-inducible ES cell line and transgenic mouse, both of which overexpress phosphomimic mutant of RXRα (T82D/S260D). Interestingly, the transcriptional activities of Retinoid X Receptor Response Element (RXRE) were significantly reduced in the Mouse Embryonic Fibroblasts (MEFs) derived from the transgenic mice, suggesting that the retinoid signaling via RXRα were impaired in the mice. Moreover, the development of liver tumors induced by liver carcinogen diethylnitrosamine (DEN) was enhanced in the transgenic mice that overexpress T82D/S260D protein in the liver. Notably, the increased liver tumors in the transgenic mice resulted from the promotion of cell cycle progression, not the inhibition of apoptosis. Interestingly, expression of β-catenin and its target genes, cyclin D1 and c-myc, were increased in transgenic liver tumors, although the expression of retinoid-related genes, such as RARβ, p21 and p27, were not altered compared with control mice. These results suggest that the phospho-modification of RXRα may promote the development of DEN-induced liver tumors through the activation of β-catenin signaling pathways in mice.
Citation Format: Hiroyasu Sakai, Yohei Shirakami, Masahito Shimizu. The role of the phosphorylated RXRα on diethylnitrosamine-induced liver tumorigenesis in mice. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4052.
Abstract 4059: Molecular role of cytochrome P450 (CYP)1A2 in the regulation of hepatic and pulmonary CYP1A1 expression in mice exposed to 3-Methycholanthrene
Authors: Moorthy Bhagavatula , Maturu Paramahamsa , Wang Lihua , Jiang Weiwu 
Published: July 2016

Abstract
3-Methylcholanthrene (MC) is one of the most potent polycyclic aromatic hydrocarbons (PAHs) carcinogens known to date. PAHs are present in cigarette smoke, diesel exhausts, and charcoal broiled meats, etc. Cytochrome P450 (CYP) 1A enzymes play key roles in the activation of PAHs to carcinogenic metabolites. In this investigation, we tested the hypothesis that CYP1A2 plays a mechanistic role in the regulation of hepatic and pulmonary CYP1A1 by MC. Wild type (WT) (C57B6) and Cyp1a2_null mice were divided into two groups. Group I was treated with vehicle corn oil (CO) (8 ml/kg) and group II was treated with four doses of MC (100 μmol/kg), i.p. once daily for 4 days. Four animals from each group were sacrificed at 6, 12, 24, and 48 h, 8 and 15 days after MC withdrawal. The mRNA levels, protein content and enzyme activities of CYP1A1 and 1A2 were determined at different time points. In addition, the binding of MC-AHR-AHR nuclear translocator (ARNT) to the AHREs on the CYP1A1 promoter region was determined by chromatin immunoprecipitation (ChIP) assay in liver and lung tissues. In WT mice, ChIP experiments indicated that transcriptional activation of CYP1A1 was most pronounced at 6 h, followed by 12 h, but declined at later time points. In Cyp1a2_null mice, on the other hand, transcriptional activation of CYP1A1 persisted till 48 h. In lungs, AHR complex binding peak was observed at 12 h and declined later, but Cyp1a2 null mice showed more persistent binding till 48 h with a peak at 24 h. On the other hand, the expression of CYP1A1/1A2 at the mRNA, protein, and enzyme levels persisted for up to 48 h both in lung and liver tissues. These results suggest a mechanistic role for CYP1A2 in the molecular regulation of CYP1A1, and that transcriptional activation of CYP1A1 at 6-12 h is sufficient to result in sustained induction of CYP1A mRNA and protein expression for up to 48 h. These studies have important implications for carcinogenesis mediated by PAHs.
Citation Format: Bhagavatula Moorthy, Paramahamsa Maturu, Lihua Wang, Weiwu Jiang. Molecular role of cytochrome P450 (CYP)1A2 in the regulation of hepatic and pulmonary CYP1A1 expression in mice exposed to 3-Methycholanthrene. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4059.
Abstract 4066: The chemokine CXCL13 in lung cancers associated with environmental polycyclic aromatic hydrocarbons pollution
Authors: Wang Gui-Zhen , Cheng Xin , Zhou Guang-Biao 
Published: July 2016

Abstract
More than 90% of lung cancers are caused by cigarette smoke and air pollution, with polycyclic aromatic hydrocarbons (PAHs) as key carcinogens. In Xuanwei City of Yunnan Province the lung cancer incidence is among the highest in China attributed to smoky coal combustion-generated PAH pollution. Here we screened for abnormal inflammatory factors in non-small cell lung cancers (NSCLCs) from Xuanwei and control regions (CR) where smoky coal was not used, and found that a chemokine CXCL13 was overexpressed in 63/70 (90%) of Xuanwei NSCLCs and 44/71 (62%) of smoker and 27/60 (45%) of non-smoker CR patients. CXCL13 overexpression was associated with the region Xuanwei and cigarette smoke. The key carcinogen bezo(a)pyrene (BaP) induced CXCL13 production in lung epithelial cells and in mice prior to development of detectable lung cancer. Deficiency in Cxcl13 or its receptor, Cxcr5, attenuated BaP-induced lung cancer in mice, demonstrating CXCL13's critical role in PAH-induced lung carcinogenesis.
Citation Format: Gui-Zhen Wang, Xin Cheng, Guang-Biao Zhou. The chemokine CXCL13 in lung cancers associated with environmental polycyclic aromatic hydrocarbons pollution. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4066.
Abstract 4068: Role of cytochrome P450 (CYP)1A2 in the molecular regulation of CYP1A1 by the carcinogen, 3-methylcholanthrene (MC) in mouse heptoma cells (hepa-1)
Authors: Kondraganti Sudha , Chu Chun , Moorthy Bhagavatula 
Published: July 2016

Abstract
Cytochrome P4501A (CYP1A) enzymes play important roles in the activation of PAHs such as 3-methylcholanthrene (MC) to carcinogenic DNA-binding metabolites. We reported earlier that MC causes persistent induction of hepatic and pulmonary CYP1A1 in mice for several weeks after MC withdrawal, and that the phenomenon of sustained hepatic CYP1A1 induction is lost in Cyp1a2-null mice. In this study, we tested the hypothesis that MC elicits induction of persistent CYP1A1 induction in hepa-1 cells, and that CYP1A2 contributes mechanistically to this phenomenon. Hepa-1 cells were treated with the MC (2.5 μM), or dimethylsulfoxide (DMSO) as control, and at selected time points, CYP1A1 promoter activity, CYP1A1 enzyme activities, contents, and CYP1A1 mRNA levels were studied. A 24 h treatment induced the CYP1A1 promoter activity, CYP1A1 mRNA, and ethoxyresorufin O-deethylase (EROD) activity by 2-, 1000-, and 15-fold, respectively. The induction was sustained for 4-5 days. MC persistently induced CYP1A1 apoprotein level as well. Electrophoretic mobility shift assay indicated that MC induced a nuclear protein that bound to aryl hydrocarbon response elements in the CYP1A1 promoter region. Transfection of CYP1A2 siRNA resulted in knockdown of CYP1A2 mRNA by 70%, but a statistically significant increase of basal CYP1A1 mRNA by 35-40%. The induction of CYP1A1 promoter activity, CYP1A1 mRNA, CYP1A1 protein, and EROD activity by MC were not affected by CYP1A2 siRNA at the 24 h time point, but was significantly attenuated by CYP1A2 siRNA on day 5. These results suggest that CYP1A2, possibly via a metabolite, contributes to the sustained induction of CYP1A1 by MC in hepa-I cells. Further investigations into the mechanisms of persistent induction of CYP1A1 by MC could lead to novel preventative/therapeutic strategies against PAH-mediated carcinogenesis in humans.
Citation Format: Sudha Kondraganti, Chun Chu, Bhagavatula Moorthy. Role of cytochrome P450 (CYP)1A2 in the molecular regulation of CYP1A1 by the carcinogen, 3-methylcholanthrene (MC) in mouse heptoma cells (hepa-1). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4068.
Abstract 4071: Targeted disruption of T-cell protein tyrosine phosphatase in mouse epidermis reveals its critical role in chemically-induced skin carcinogenesis
Authors: Lee Hyunseung , Kim Mihwa , Morales Liza D. , Slaga Thomas J. , DiGiovanni John , Kim Dae J. 
Published: July 2016

Abstract
Environmental factors such as chemical toxicants contribute to the development of skin cancer by creating mutations in housekeeping genes and proto-oncogenes which disrupt intracellular signaling mechanisms. One vital signaling mechanism is tyrosine phosphorylation signaling. Phosphotyrosine signaling is regulated by the counter-activities of protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs). Recently we reported TC-PTP (PTPN2) is critical regulator of STAT3 signaling in mouse keratinocytes. To assess the role of TC-PTP in skin carcinogenesis, we generated epidermal-specific TC-PTP-deficient (K14Cre.PTPN2fl/fl) transgenic mice. Loss of TC-PTP led to a desensitization to tumor initiator 7,12-dimethylbenz[a]anthracene (DMBA)-induced apoptosis both in vivo epidermis and in vitro keratinocytes. TC-PTP deficiency in epidermis resulted in a significant increase in epidermal thickness and hyperproliferation (assessed by bromodeoxyuridine (BrdU) labeling index) compared to control mice following treatment with the tumor promoter, 12-O-tetradecanoylphorbol-13-acetate (TPA). Consistently, primary keratinocytes derived from TC-PTP-deficient mice showed a faster growth rate. To further investigate the role of TC-PTP in skin carcinogenesis, TC-PTP-deficient mice were subjected to two-stage skin carcinogenesis analysis. TC-PTP-deficient mice showed a shortened latency of tumor development and significantly increased numbers of tumors compared to control mice, demonstrating TC-PTP deficiency predisposes mice to skin carcinogenesis. The data reveals TC-PTP may be a novel potential target for the prevention of skin cancer due to its role in the regulation of proliferation and apoptosis in epidermis.
Citation Format: Hyunseung Lee, Mihwa Kim, Liza D. Morales, Thomas J. Slaga, John DiGiovanni, Dae J. Kim. Targeted disruption of T-cell protein tyrosine phosphatase in mouse epidermis reveals its critical role in chemically-induced skin carcinogenesis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4071.