bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3213: Evaluation of porphyrin biodistribution for use in photodynamic therapy of retinoblastoma in transgenic mice
Authors: Poyer Florent , Hugeut Samuel , Lemaitre Stéphanie , Madar Olivier , Thomas Carole D , Maillard Philippe , Teulade-Fichou Marie-Paule , Cassoux Nathalie , Doz François , Rezai Keyvan 
Published: August 2018

Abstract
Background: Porphyrins are a group of heterocyclic macrocycle organic compounds. They have shown good efficiency in the photodynamic treatment of tumors in the last twenty years. The photodynamic therapy could be an alternative treatment for retinoblastoma using a photosensitizer with low dark toxicity and low mutagenic properties unlike the conventional chemotherapies. The objectives of this study were to develop a photosensitizer in our lab which is a diethylene glycol mannoconjugated tetraphenyl porphyrin (TPP, MW: 1413.6) and to determine the optimal interval time for photodynamic therapy using the concentration of TPP in eye and blood samples of mice. Materials and method: Transgenic mice developed bilateral retinoblastoma from the retina since 4 weeks of age to 16 weeks of age (tumors fill the ocular globe and the mice will be sacrificed for ethic purpose). The evaluation of the biodistribution of our TPP was realized to know the best drug-light interval to perform the photodynamic therapy. For this purpose, an intraperitoneal injection of 200 µl at 5.25 mg/ml in PEG 400/physiological serum (1:1, v/v) was performed on the LHbetaTag transgenic mice. At different time intervals (8h, 24h, 40h, 48h, and 72h) following injection, the mice were sacrificed and the eyes and blood were collected. TPP in eye samples were extracted in methanol and the level of TPP was measured by ultra-performance liquid chromatography with tandem mass spectrometry (UPLC-MS/MS) analysis (0.5-100 ng/mL). The level of TTP in blood samples was quantified after protein precipitation by UPLC-MS/MS method (5.00-1000 ng/mL).
Results: We observed a time dependency accumulation of TPP in eyes with observed Tmax=48 hours. TPP serum concentrations decreased by the same manner up to 48 h. The determination of drug-light interval allowed us to perform the light delivery when the TPP level is highest (48 h) in the ocular tumor tissue (retinoblastoma).
Conclusions: Our TPP had a good in vitro photocytotoxicity at very low doses and showed a good efficacy in vivo with subcutaneous patient derived retinoblastoma xenografts in immunodeficient mice. The knowledge of Tmax and this interval is essential to realize the photodynamic therapy with the better efficiency, the final goal being to eradicate the retinoblastoma from the retina.
Citation Format: Florent Poyer, Samuel Hugeut, Stéphanie Lemaitre, Olivier Madar, Carole D Thomas, Philippe Maillard, Marie-Paule Teulade-Fichou, Nathalie Cassoux, François Doz, Keyvan Rezai. Evaluation of porphyrin biodistribution for use in photodynamic therapy of retinoblastoma in transgenic mice [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 3213.
Abstract 3214: FePt nanoparticles overcoming radiotherapy resistance in hCtr-1 high expression cells via mitochondria targeting
Authors: Tsai Tsung-Lin , Kuo Macus Tien , Wang Jen-Ya , Shin Wan-Li , Chen Helen H. W. , Su Wu-Chou 
Published: August 2018

Abstract
The glutathione (GSH) overexpression small-cell-lung-cancer cell lines, SR3A-13 and SR3A-14, transfected with recombinant DNA encoding γ-glutamylcysteine synthetase (γ-GCSh), are radiation resistant. However, they are more sensitive to cisplatin treatment, compared with parental cell (SR3A)1. In addition to be a copper transporter, the hCtr-1 is also a transporter for platinum (Pt)-based agents. Therefore, the cellular uptake of cisplatin is enhanced by the upregulation of human copper transporter 1 (hCtr-1) at the cell membrane. We have synthesized an alloy FePt nanoparticles (FePt NPs) that generated excellent contrast effects in both CT and MRI images2. Interestingly, the uptake of FePt NPs by SR3A-13 and -14 cells was 3-3.5 fold higher than that of SR3A cells, measured with inductively coupled plasma optical emission spectrometry (ICP-OES) and transmission electron microscopy (TEM). Because intracellular NPs have been shown to generate reactive oxygen species (ROS) and overproduction of ROS may enhance the efficacy of radiotherapy, we sought to explore whether treatment with the alloy FePt NPs can reverse the radiation resistance in SR3A-13 and -14 cells. We found co-treatment with the alloy FePt NPs and radiation effectively reduce the survivals of these 2 cells. Furthermore, we found an alternation in mitochondrial appearance accompanied with low signal of Tetramethylrhodamine, methyl ester (TMRM), indicating a malfunction is induced in mitochondria. We conclude that FePt NPs are able to overcome radiation resistance in hCtr-1 high expression cells via mitochondria targeting.
Citation Format: Tsung-Lin Tsai, Macus Tien Kuo, Jen-Ya Wang, Wan-Li Shin, Helen H. W. Chen, Wu-Chou Su. FePt nanoparticles overcoming radiotherapy resistance in hCtr-1 high expression cells via mitochondria targeting [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 3214.
Abstract 3225: Cutaneous nevi and cancer risk among US women
Authors: Li Xin , Wu Wenting , Giovannucci Edward , Stampfer Meir J. , Gao Xiang , Han Jiali 
Published: August 2018

Abstract
Background: Longer telomeres have been linked to elevated cutaneous nevus number. Recently, a large Mendelian randomization study identified a positive association between telomere length and risk of cancer. We hypothesized that higher nevus count, as a phenotypic marker of longer telomere length, may be associated with increased risk of cancer development.
Methods: We prospectively examined the association between nevus count and total as well as site-specific cancer risk among participants in the Nurses' Health Study (NHS, 1986-2012) and the Nurses' Health Study 2 (NHS2, 1989-2013).
Results: During 3,941,477 person-years of follow-up, we documented a total of 24,428 cancer cases (16,297 in the NHS and 8,131 in the NHS2). Compared to participants who had no nevi, the multivariate HRs were 1.08 (95%, 1.05-1.11) for women with 1-5 nevi, 1.15 (95%, 1.09-1.21) for those who had 6-14 nevi, and 1.26 (95%, 1.18-1.34) for those with 15 or more nevi (p trend &lt; 0.0001). We did not observe significant interactions between the number of nevi and other covariates in the multivariable-adjusted model. We also conducted secondary analyses by excluding 1) only melanoma and 2) both melanoma and breast cancer from the outcomes of interest, respectively. The results were very similar to those of our primary analysis using all cancer sites. For individual cancer sites, most of the associations with mole counts were positive but not statistically significant.
Conclusion: We identified the number of cutaneous nevi as a phenotypic marker associated with cancer risk, which may possibly be explained by telomere biology.
Citation Format: Xin Li, Wenting Wu, Edward Giovannucci, Meir J. Stampfer, Xiang Gao, Jiali Han. Cutaneous nevi and cancer risk among US women [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 3225.
Abstract 3232: Circulating sCD27 and sCD30 in samples collected fifteen years apart and non-Hodgkin lymphoma risk: Findings from the CLUE-I and CLUE-II cohorts
Authors: Purdue Mark P. , Lan Qing , Hoffman-Bolton Judith , Hildesheim Allan , Strickland Paul , Visvanathan Kala , Rothman Nathaniel 
Published: August 2018

Abstract
Elevated serum levels of the immune activation markers sCD27 and sCD30 have been consistently associated with increased future risk of non-Hodgkin lymphoma (NHL). However, past studies could not clarify patterns of these markers over time preceding diagnosis, given their use of a single banked sample per participant. To address this question, we conducted a nested case-control study within the CLUE-I and CLUE-II cohorts including 102 case-control matched pairs with two banked samples per participant, collected fifteen years apart. The CLUE-II sCD27 concentrations among cases were higher than in the earlier CLUE-I samples (P&lt;0.0001), whereas no systematic difference was observed for controls (P=0.89). The sCD27 increase was greater for cases diagnosed less than 10 years vs. 10+ years after CLUE-II enrollment (P = 0.0007). For sCD30, an increase between samples was observed for both cases (P = 0.0002) and controls (P=0.02), and the magnitude of increase among cases did not significantly differ across the two follow-up periods (P = 0.12). In comparison to having low (below-median) sCD27 levels in both CLUE-I and CLUE-II samples, associations with NHL were observed for having low CLUE-I sCD27 and high CLUE-II sCD27 (“low / high”; odds ratio 2.4, 95% confidence interval 1.0-6.2) as well as having high sCD27 levels in both samples (“high / high”; 2.1, 1.0-4.4). For sCD30, only the “high-high” category was associated with NHL (2.1, 0.9-5.0). The “low-high” sCD27 association was apparent only for cases diagnosed less than 10 years after CLUE-II (4.1, 1.3-13.0), while the “high-high” associations were consistent across follow-up periods. Our findings suggest that multiple factors may underlie NHL associations with these markers; rising sCD27 closer to diagnosis is likely driven by occult disease, whereas associations with stable elevated analyte levels may reflect etiologically relevant effects.
Citation Format: Mark P. Purdue, Qing Lan, Judith Hoffman-Bolton, Allan Hildesheim, Paul Strickland, Kala Visvanathan, Nathaniel Rothman. Circulating sCD27 and sCD30 in samples collected fifteen years apart and non-Hodgkin lymphoma risk: Findings from the CLUE-I and CLUE-II cohorts [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 3232.
Abstract 3243: Associations of polyomavirus seroreactivity with AIDS-related non-Hodgkin's lymphoma
Authors: Song Minkyo , Bender Noemi , Goedert James J. , Winkler Cheryl A. , Brenner Nicole , Waterboer Tim , Rabkin Charles S. 
Published: August 2018

Abstract
Background: Human polyomaviruses have a suspected role in carcinogenesis. In the setting of human immunodeficiency virus (HIV) infection, coinfection with MCV polyomavirus is associated with high risk of Merkel cell carcinoma. A role in lymphomagenesis has also been suggested by studies in the general population, but there are no prior studies in individuals with the acquired immunodeficiency syndrome (AIDS).
Methods: We measured antibodies against 11 common polyomaviruses in archived serum and plasma samples from two prospective cohort studies of HIV infection. Patients with incident (n=28) and prevalent (n=38) AIDS-related non-Hodgkin lymphoma (NHL) were matched by age, sex, and CD4 count to 67 HIV-positive AIDS-free controls. Seroreactivity was measured by fluorescent bead-based multiplex serology, quantified as median fluorescence intensity (MFI). Logistic regression models were used to estimate adjusted odds ratios (ORs) and 95% confidence intervals (95% CIs) for NHL risk. Multinomial logistic regression compared incident and prevalent NHL cases to lymphoma-free controls and heterogeneity between case groups was evaluated by Wald tests. Differences in MFI were assessed by Kruskal-Wallis tests. Based on log-transformed MFI values for 15 masked duplicate samples, estimated coefficients of variation (CV) were &lt;20% and intraclass correlation coefficients (ICC) were &gt;90% for all antibodies except LPV (CV 29%, ICC 67%).
Results: Cases had significantly lower prevalence of antibodies to WU polyomavirus than lymphoma-free controls (64% vs. 85%), with OR 0.28 (95% CI 0.12-0.68). Cases had non-significantly lower prevalence of antibodies to JC, TSV, MCV and KI polyomaviruses (ORs 0.42-0.71); similar prevalence of antibodies to BK, HPyV6 and HPyV7 polyomaviruses (ORs 0.98-1.18); and non-significantly higher prevalence of antibodies to HPyV10, LPV and HPyV9 polyomaviruses (ORs 1.35-1.77). MFIs for anti-WU antibodies were also lower for cases (median 552.6, interquartile range [IQR] 140.3-1298.3) than controls (median 1096.3, IQR 410.3-2044.3; p-value 0.047). The association of anti-WU antibody with NHL was stronger in samples obtained post-diagnosis (OR 0.18, 95% CI 0.07-0.48) than pre-diagnosis (OR 0.66, 95% CI 0.19-2.31; p-heterogeneity=0.037).
Conclusion: Our data do not directly implicate known polyomaviruses as lymphomagenic in the setting of HIV-associated immunodeficiency. Nevertheless, impaired antibody response to WU may be a harbinger of AIDS-related lymphoma.
Citation Format: Minkyo Song, Noemi Bender, James J. Goedert, Cheryl A. Winkler, Nicole Brenner, Tim Waterboer, Charles S. Rabkin. Associations of polyomavirus seroreactivity with AIDS-related non-Hodgkin's lymphoma [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 3243.
Abstract 3251: TaqMan Advanced miRNA cDNA Synthesis Kit to simultaneously study expression of miRNA and mRNA and to detect somatic mutations by qPCR
Authors: Hayashibara Kathleen , Veereshlingam Harita , Buchholz Malte 
Published: August 2018

Abstract
MicroRNAs (miRNA) are a class of small non-coding RNAs (approximately 21 nt long) that bind complementary sequences in target mRNAs to specifically regulate gene expression. Aberrant regulation of miRNAs and their targets has been associated with several diseases including cancer. The relationship between miRNA and mRNA has been found to be important in cancer development and progression. Simultaneous expression studies of miRNA and mRNA and detection of mutations in mRNA transcripts can be valuable in understanding molecular mechanisms that have an underlying role in various diseases. We demonstrate the technical verification of a novel method to reverse-transcribe and pre-amplify miRNA and mRNA from sample-limiting serum research samples using the TaqMan® Advanced miRNA cDNA Synthesis Kit. Based on results from previous studies, a signature of 49 mRNA and 37 miRNA targets has been identified that may help distinguish between benign and malignant pancreatic tissues. In this study, these targets and an additional set of transcript mutations were analyzed in serum from normal and test samples. TaqMan assays for miRNA and mRNA targets and custom TaqMan Mutation Detection Assays were placed on TaqMan Array Cards to facilitate investigation of several samples in a single experiment. Results demonstrate that transcript mutations can be detected and miRNA and mRNA targets can be reliably quantified from a single reverse transcription reaction. (For research use only. Not for use in diagnostic purposes.)
Citation Format: Kathleen Hayashibara, Harita Veereshlingam, Malte Buchholz. TaqMan Advanced miRNA cDNA Synthesis Kit to simultaneously study expression of miRNA and mRNA and to detect somatic mutations by qPCR [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 3251.
Abstract 3255: The roles of ALDH2, ADH1B and ADH1C gene polymorphism in predicting upper digestive tract multiple primary malignancies in head and neck cancer patients
Authors: Huang Shiang-Fu , Chien Huei-Tzu , Cheng Sou-De , Liao Chun-Ta , Wang Hung-Ming 
Published: August 2018

Abstract
Head and neck cancer was closely related with habitual use of cigarette and alcohol. The genes involving in the metabolism of alcohol are reported to play roles in increasing risks of head and neck cancer. In this study, we investigated the single nucleotide polymorphisms (SNPs) of alcohol metabolizing enzymes (ALDH2, ADH1B and ADH1C) in their distributions among different tumor subsites and their risks of developing multiple primary cancers. We recruited 659 male head and neck cancer patients between Mar 1996 and Feb 2017. Four hundred and twenty-seven normal controls were also recruited. The SNPs in ALDH2 (rs671), ADH1B (rs1229984) and ADH1C (rs698) were analyzed by Taqman PCR primers and TaqMan probes synthesized by Applied Biosystems (Foster City, CA). Genotyping was performed using the Taqman-based allelic discrimination method on an Applied Biosystems 7500 Real-Time Polymerase Chain Reaction System (Applied Biosystems, Foster City, CA). The A allele carriers than G/G homozygotes in ALDH2 is significantly higher in oral cavity cancer (p = 0.016), oropharynx (p = 0.018) and hypopharynx cancer (p = 0.051) than normal population but not in tonsillar cancer (p = 0.099). In ADH1B, the G allele carriers is significantly higher than A/A homozygotes in oropharynx (p = 0.012), tonsillar cancer (p = 0.050) and hypopharynx cancer (p &lt; 0.001) than normal population but not in oral cavity cancer (p = 0.406). We did not observe ADH1C (rs698) SNP significantly related with HNSCC tumor subsites (p &gt; 0.05). For ALDH2 (A allele carriers vs G/G homozygotes) and ADH1B (G allele carriers vs A/A homozygotes), they significantly increased risks to develop multiple primary cancers in upper digestive tract (p &lt; 0.001, OR [95% confidence interval, C.I.]: 5.358 [2.565-11.195]. and p &lt; 0.001, OR [95% C.I.]: 2.907 [1.598 - 5.290]). Conclusion:ALDH2 (rs671) A allele carriers and ADH1B (rs1229984) G allele carriers had higher risks of developing multiple primary cancers in upper digestive tract. For those with high risk allele carriers, routine screening of upper digestive tract including laryngoscope and esophagoscope is suggested to detect new primaries early.
Citation Format: Shiang-Fu Huang, Huei-Tzu Chien, Sou-De Cheng, Chun-Ta Liao, Hung-Ming Wang. The roles of ALDH2, ADH1B and ADH1C gene polymorphism in predicting upper digestive tract multiple primary malignancies in head and neck 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 3255.
Abstract 3279: Comprehensive analysis of small nucleolar RNAs across in human cancers
Authors: Gong Jing , Li Yajuan , Liu Chunjie , Xiang Yu , Guo An-yuan , Lin Chunru , Han Leng 
Published: August 2018

Abstract
Recent studies demonstrated that small nucleolar RNAs (snoRNAs) play important roles in tumorigenesis. We systematically investigated the expression landscape and clinical relevance of snoRNAs in &gt;10,000 samples across 31 cancer types. We observed overall elevated expression of snoRNAs and their ribonucleoproteins in multiple cancer types. We showed complex regulation of snoRNA expression by their host genes, copy number variation, and DNA methylation. Unsupervised clustering revealed that the snoRNA expression subtype is highly concordant with other molecular/clinical subtypes. We further identified 46 clinically relevant snoRNAs and experimentally demonstrated functional roles of SNORD46 in promoting cell proliferation, migration, and invasion. We developed a user-friendly data portal, SNORic, to benefit the research community. Our study highlights the significant roles of snoRNAs in the development and implementation of biomarkers or therapeutic targets for cancer and provides a valuable resource for cancer research.
Citation Format: Jing Gong, Yajuan Li, Chunjie Liu, Yu Xiang, An-yuan Guo, Chunru Lin, Leng Han. Comprehensive analysis of small nucleolar RNAs across in human cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3279.
Abstract 3280: Utah somatic variant calling pipeline featuring multi-sample joint calling, variant-graph based accurate allele frequency estimation and subclone analysis
Authors: Qiao Yi , Huang Xiaomeng , Lee Dillon , Farrell Andrew , Nicholas Thomas , Pederson Brent , Quinlan Aaron , Marth Gabor 
Published: August 2018

Abstract
Current tumor variant detection software tools are focused on the identification of somatic mutations in a single tumor sample (e.g. the primary tumor) compared to normal control tissue, and are not adequate for studies where multiple samples from the same patient, either at consecutive time points or at different metastatic sites are collected. Here we present a software framework that facilitates simultaneous analysis of such multi-sample datasets.
Our framework utilizes our FreeBayes variant caller for jointly calling all tumor samples and normal controls from the patient. This ensures that even very low frequency mutations are called because read evidence is aggregated across all samples; and that allele frequency information for a called somatic variant is provided uniformly for all samples. Short and medium-length INDELs, and structural variants are identified by our RUFUS software, a new reference-free mutation calling algorithm for both germline and somatic mutation detection, with extremely high sensitivity and specificity. We use our Graphite tool, a graph-genome based read realignment algorithm, to eliminate false positive somatic calls i.e. inherited variants masquerading as somatic mutations, and to substantially increase accuracy of allele frequency estimation of the true somatic calls, a feature critical for downstream subclone analysis. In addition, we use the FACETS package for CNV and LOH analysis, also critical for downstream subclone analysis.
Finally, we utilize SubcloneSeeker, our algorithm to reconstruct the evolution of the cancer at the subclonal level from the somatic variant allele frequencies, to understand how the tumor evolved over time, in response to multiple courses of treatment, or over space, across multiple metastatic sites. We demonstrate the use of this pipeline in published and ongoing studies involving longitudinal and multi-site tumor sample datasets.
Citation Format: Yi Qiao, Xiaomeng Huang, Dillon Lee, Andrew Farrell, Thomas Nicholas, Brent Pederson, Aaron Quinlan, Gabor Marth. Utah somatic variant calling pipeline featuring multi-sample joint calling, variant-graph based accurate allele frequency estimation and subclone analysis [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 3280.