bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 267: GeoSurveillance of invasive cervical cancer incidence by counties in the state of Maryland
Authors: Peprah Sally , Curriero Frank , D'Souza Amber
Published: July 2017

Background: Invasive cervical cancer (ICC) is a highly preventable cancer whose rates have dramatically declined over the past few decades. In spite of the progress made, new ICC cases are recorded annually in Maryland and in other parts of the United Sates. We assessed if ICC incidence varied significantly 2005-2012 and across counties within the state of Maryland.

Methods: Using a discrete Poisson model we evaluated significant space-time clusters of both high and low ICC incidence rates over a retrospective 10-year period. All analyses were conducted at the county level, using 2-year aggregates of time. We adjusted for age, percent minority, cervical cancer screening rates, median income, obesity as well as smoking rates within each county in our final cluster detection

analysis.

Results: ICC was 13.1 per 100,000 female population and did vary by county and over the 10-year period assessed. We identified five significant space-time clusters of ICC incidence, three of which were clusters of higher than expected rates. The most likely cluster identified was a cluster of low ICC incidence [aRR=0.08, p-value<0.01] observed for the period 2009-2012 and comprised six high-income suburban counties. The other cluster of low rate [aRR=0.41, p-value<0.01], which was a secondary cluster, was observed for the same time period, 2009-2012 in three high to moderate-income suburban counties. There were two clusters of high ICC incidence, observed for recent time periods. One cluster [aRR=1.74, p-value<0.01], which was made up of a single moderate to low-income urban county was identified for the period 2009-2012. The other cluster of elevated rates [aRR=2.47, p-value<0.01] was identified in a suburban moderate-income county for the period 2011-2012. Additionally, for the period 2005-2008 we identified a historical cluster of elevated incidence [aRR=2.53, p-value<0.01].

Conclusion: Overtime some counties in Maryland have experienced significantly lower rates of disease than expected. However there are more recent clusters of higher than expected rates of disease, which are not explained by the county level variables adjusted for. These clusters of high rates need to be further examined and addressed.

Citation Format: Sally Peprah, Frank Curriero, Amber D'Souza. GeoSurveillance of invasive cervical cancer incidence by counties in the state of Maryland [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 267. doi:10.1158/1538-7445.AM2017-267
Abstract 2688: Multiplex IHC detection of immune checkpoint receptors in the tumor microenvironment
Authors: Ziello Jennifer E. , Klein Sarah R. , Alonzo Emily , Haack Herbert
Published: July 2017

As immune checkpoint blockade has been shown to partially reverse the exhausted T cell phenotype and consequently lead to a decrease in tumor burden, there is a need for an understanding of this T cell type. Using recently developed, highly validated antibodies, we have developed a fluorescent multiplex, TSA-based assay in order to examine the interaction of PD-L1 with PD-1-expressing exhausted T cells in various tumor types. Here, we construct a seven-color multiplex panel in order to simultaneously visualize cytokeratin (the tumor mask), DAPI (nuclear counterstain), CD8 (cytotoxic T cell marker), the exhausted T cell markers PD-1, Tim-3 and Lag-3, and the ligand for PD-1, PD-L1. This technique not only enabled the concurrent detection of these markers, but also provided high-resolution visualization of interactions between PD-1-expressing CD8+ T cells and PD-L1-expressing CD68+ macrophages in the tumor microenvironment. The seven-plex panel was applied to FFPE tumor microarrays (TMAs) consisting of breast, lung and ovarian tumor tissue and each core was subsequently analyzed for the distribution, co-localization, frequency and proximity of these targets in relation to one another. While we often visualized co-expression of Lag-3 and PD-1 on T cells, Tim-3 was frequently observed on PD-L1+ macrophages in several tumor types. This data provides valuable insight into the co-expression profiles of these markers in multiple tumor types and has implications for the use of combination therapies that aim to target both the innate and adaptive immune systems.

Citation Format: Jennifer E. Ziello, Sarah R. Klein, Emily Alonzo, Herbert Haack. Multiplex IHC detection of immune checkpoint receptors in the tumor microenvironment [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 2688. doi:10.1158/1538-7445.AM2017-2688
Abstract 269: The descriptive epidemiology of gynecologic cancers: an international comparison of incidence, survival and mortality
Authors: Zaidi Zoubida , Cherif Mokhtar Hamdi
Published: July 2017

Introduction: Gynecologic Cancers are the most common cancers in women, in 2012, Cervical Cancer (CC) is ranking as the fourth with an estimated 528.000 new cases and Ovarian Cancer (OC) is the seventh most common for females with nearly 239.000 new cases worldwide.

Aim: this communication presents the latest international descriptive epidemiological data for invasive GC, including incidence, survival and mortality in the worldwide.

Methods: -The incidence and mortality statistics presented for GC worldwide were taken from the International Agency for Research on Cancer IARC: * the Cancer Incidence in five Continents Vol X and * GLOBOCAN database, 2012.

-The data of cancer survival are taken from: * Cancer survival in five continents, a worldwide population-based study (CONCORD) version 2, 1995-2009. Estimated five-year net survival, adjusted for background mortality by single year of age, sex, calendar year in each country.

Results: CC is the most common cancer among women in 45 countries mainly in sub-Saharan Africa, part of Asia and some countries in Central and South America, the lowest incidence rates in western Europe, North America, Australia and the eastern Mediterranean. Almost 55% of all new cases of OC occurred in countries very high level of human development mainly northern Europe and America and Oceanic, Africa presents the lowest incidence.

-Data for CC are available for 602 225 women, CC survival was 50% or higher in most countries, except for Libya (Benghazi, 39%) and India (Karunagappally, 46%). During 2005-09, age-standardised 5-year net survival was 70% or higher in Iceland, Mauritius, Norway, South Korea, and Taiwan, for Qatar is also above 70% (based on only 16 cases and is not age-standardised).

-Data for ovarian cancer are available for 779 302 women, during 2005-09, age-standardised 5-year net survival was 40% or higher in Ecuador, the USA, nine countries in Asia, and eight countries in Europe. Survival in other countries was mostly in the range 30-40%, except for Libya (22%).

Conclusions: The evolution of cancers in women shows a consistent and very striking pattern during the epidemiological transition with rapid declines in the incidence of cervical cancer. Comparison of population-based cancer survival CONCORD study 2 showed very wide variations in survival from gynecologic cancer worldwide.

Note: This abstract was not presented at the meeting.

Citation Format: Zoubida Zaidi, Mokhtar Hamdi Cherif. The descriptive epidemiology of gynecologic cancers: an international comparison of incidence, survival and mortality [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 269. doi:10.1158/1538-7445.AM2017-269
Abstract 2690: MK2 pathway blockade inhibits inflammatory cytokine production and colorectal cancer growth and invasion
Authors: Ray Anita L. , Peretti Amanda S. , Johnson Wade , Gan Gregory , Beswick Ellen J.
Published: July 2017

Introduction: Colorectal cancer is the third most common malignancy diagnosed for both men and women in the United States of America. High levels of inflammatory cytokines in colorectal tumors cause increased growth and invasion and carry a higher risk of metastasis. Identifying new targets to control inflammation is important for developing improved treatment approaches. Mitogen-activated protein kinase-activated protein kinase 2 (MK2) is a regulator of pro-inflammatory cytokines that may promote colorectal tumor progression. MK2 signaling is known to induce IL-1, IL-6, and TNF-α production. These pro-inflammatory cytokines are associated with CRC development, invasion, and metastasis. We hypothesized that the MK2 pathway could be an important component of CRC growth, invasion and tumor regrowth.

Methods: To investigate this pathway, CT26 CRC cells were examined. Cells were flank-injected into Balb/c mice with and without MK2 inhibitor treatment. At day 19 after tumor injection, tumors were harvested and measured using calipers. Cytokines were quantitated by multiplex bead array in organ culture supernatants and in supernatants from tumor cells plated in fibronectin coated wells. In culture, tumor cell invasion was measured in scratch wound assays containing matrigel.

Results: Treating CT26 cells with MK2 inhibitors markedly reduced tumor growth in mice by a mean of 60% compared to vehicle control treated cells. Inflammatory cytokines were also dramatically decreased with MK2 inhibition compared to controls by up to 80%. Cytokines affected included both known MK2 downstream cytokines (IL-1, IL-6, and TNF-α) and also chemokines such as MIP-1α and MCP-1 in both supernatants from cultured tumor cells and in organ culture supernatants. MK2 inhibition also decreased invasion of tumor cells in a cytokine dependent manner.

Conclusions: The MK2 pathway regulates production of multiple pro-inflammatory cytokines in colorectal tumors, including several previously unreported chemokines. Inhibition of this pathway markedly decreases tumor growth and invasion. Thus, MK2 may be a promising tumor target to prevent colorectal cancer progression.

Citation Format: Anita L. Ray, Amanda S. Peretti, Wade Johnson, Gregory Gan, Ellen J. Beswick. MK2 pathway blockade inhibits inflammatory cytokine production and colorectal cancer growth and invasion [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 2690. doi:10.1158/1538-7445.AM2017-2690
Abstract 2696: PD-1 antibody treatment induces gut microbiota changes in CT-26 colon cancer syngeneic model
Authors: Ding Jian , Mao Binchen , Shi Qian
Published: July 2017

The gut microbiota plays an important role in shaping systemic immune response. One novel frontier in cancer research is investigating how the gut microbiota change immune response and influence the efficacy of anticancer immunotherapy drugs; this has been reported in CTLA4 and PD-L1 antibody treatment, both in laboratory and clinical settings. One recent study reported that composition of patient`s gut microbes appears to be a determining factor for immunotherapy, at least in melanoma patients. These findings shed light on the potential use of gut microbial as a biomarker for responders in cancer immunotherapy and even as a novel treatment.

Here, we evaluated the gut microbiota profiling upon PD-1 antibody (RMP1-14) treatment in CT-26 colon cancer syngeneic mouse model. Fresh feces were collected at different time points before and after treatment, snap frozen and sent for 16s RNA sequencing for microbiome profiling. Our results identified top 25 abundant taxa in genus level in CT-26 feces. Significant abundance changes were observed in several genera after PD-1 antibody treatment, especially in Akkermansia. These findings indicate that immunotherapy like PD-1 antibody can induce the profile changes of gut microbiota in CT-26 model.

Furthermore, we also investigated the correlation of gut microbiome with immune- microenvironment and the efficacy upon IO therapy, as well as the possibility to utilize microbiota profiling as a quality control step that may help to explain the variability observed in many syngeneic studies.

Citation Format: Jian Ding, Binchen Mao, Qian Shi. PD-1 antibody treatment induces gut microbiota changes in CT-26 colon cancer syngeneic 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 2696. doi:10.1158/1538-7445.AM2017-2696
Abstract 2697: A role for the membrane type-1 matrix metalloproteinase in the transcriptional regulation of carcinogen-induced inflammasome components
Authors: Sheehy Samuel , Annabi Borhane
Published: July 2017

BACKGROUND : Signal transducing functions driven by the cytoplasmic domain of membrane type-1 matrix metalloproteinase (MT1-MMP) are believed to regulate many inflammation-mediated cancer cell functions including migration, proliferation, and survival. Besides the upregulation of the inflammation biomarker cyclooxygenase (COX)-2 expression, MT1-MMP’s role in relaying the signals triggered from pro-inflammatory cues remain poorly understood.

METHODS : Here, we treated HT1080 fibrosarcoma cells with phorbol-12-myristate-13-acetate (PMA), a well-known carcinogen and inducer of COX-2 and of MT1-MMP. In order to assess the global transcriptional regulatory role that MT1-MMP may exert on inflammation biomarkers, we combined gene array screens to transiant MT1-MMP gene silencing strategy.

RESULTS : We found that MT1-MMP expression exerted both stimulatory and repressive transcriptional control of several inflammasome-related biomarkers such as IL-1B, IL-6, IL-12A, and IL-33, as well as of transcription factors such as EGR1, ELK1, and ETS1/2 in PMA-treated cells. Among the signal transducing pathways explored, silencing of MT1-MMP prevented PMA from phosphorylating Erk, IκB, and p105 KF-κB intermediates. We also highlight a signaling axis linking MT1-MMP to MMP-9 transcriptional regulation.

CONCLUSIONS : Altogether, our data evidence an important involvement of MT1-MMP in the transcriptional regulation of inflammatory biomarkers consolidating its contribution in signal transducing functions, in addition to its classical hydrolytic activity.

Citation Format: Samuel Sheehy, Borhane Annabi. A role for the membrane type-1 matrix metalloproteinase in the transcriptional regulation of carcinogen-induced inflammasome components [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 2697. doi:10.1158/1538-7445.AM2017-2697
Abstract 2706: KRT16 germline mutation associated with familial syndrome of tylosis with esophageal cancer (TOC)
Authors: Young Erin L. , Pflieger Lance , Maese Luke , Fowler Trent , Garfield Kinley , Samadder N. Jewel , Johnson Bella , Mason Clinton C. , Moore Barry , Ryanearson Shawn , Yandell Mark , Kohlmann Wendy , Schiffman Joshua D.
Published: July 2017

Tylosis (palmoplantar keratoderma) with esophageal cancer (TOC) also known as Howel-Evans syndrome has been associated with pathogenic mutations in RHBDF2. A potential TOC family was referred for clinical evaluation at the Family Cancer Assessment Clinic (FCAC) at Huntsman Cancer Institute, Salt Lake City, Utah. Multiple relatives of the proband had hyperkeratosis on the areas of skin associated with pressure and friction, especially the feet, as well as oral leukoplakia. The proband’s father, paternal aunt, paternal grandfather, and paternal great grandfather had been diagnosed with esophageal cancer. Clinical testing was unable to identify a germline mutation in RHBDFR2 that explained the observed phenotype and inheritance pattern. As part of Heritage 1K Project (University of Utah), Pediatric & Adult Cancer Section, we performed whole genome sequencing (WGS) on 5 family members, 4 that were affected with the hyperkeratosis, and 1 unaffected family member, to identify other potential genetic causes for the observed TOC phenotype. We prioritized variants via VAAST (Variant Annotation, Analysis and Search Tool). Reducing our genes of interest to those involved in palmoplantar keratoderma with PHEVOR (Phenotype Driven Variant Ontological Re-ranking Tool), we identified a pathogenic mutation: KRT16 c.379C>T p.Arg127Cys. This mutation is reported in a large palmoplantar keratoderma family (without esophageal cancer) and is listed as pathogenic in Clinvar (www.ncbi.nlm.nih.gov/clinvar). KRT16 c.379C>T p.Arg127Cys was present in each of the affected family members, but not in the unaffected relative. Our analysis is the first of its kind to suggest carriers of pathogenic variants in KRT16 are at-risk for esophageal cancer, and may benefit from esophageal surveillance. Additionally, patients presenting with a family history of esophageal cancer should be considered for germline testing for KRT16 mutations along with RHBDF2 mutations.

Citation Format: Erin L. Young, Lance Pflieger, Luke Maese, Trent Fowler, Kinley Garfield, N. Jewel Samadder, Bella Johnson, Clinton C. Mason, Barry Moore, Shawn Ryanearson, Mark Yandell, Wendy Kohlmann, Joshua D. Schiffman. KRT16 germline mutation associated with familial syndrome of tylosis with esophageal cancer (TOC) [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 2706. doi:10.1158/1538-7445.AM2017-2706
Abstract 2716: A multi-parameter assay for the detection of rare malignant cells in classical Hodgkin lymphoma
Authors: U'Ren Lance , Wu David , Fromm Jonathan R. , Stilwell Jackie , Kaldjian Eric
Published: July 2017

Background: Classical Hodgkin Lymphoma (CHL) ranks among the most frequently occurring lymphomas and is marked by Hodgkin and Reed-Sternberg (HRS) cells, frequently multi-nucleated neoplastic cells that are derived from germinal center B cells. The genetic alterations involved in the pathogenesis of this lymphoma have been difficult to study because HRS cells are rare and are surrounded by robust, non-neoplastic infiltrate, therefore they frequently represent less than 0.1% of cells within involved lymph nodes. Consequently, methods that isolate these rare cells are required to understand pathobiology of this lymphoma. We used the AccuCyte® - CyteFinder® system (RareCyte) to develop a method for detection and isolation of HRS cells.

Methods: A 6-parameter immunofluorescence assay was designed to identify HRS cells that included HRS markers (CD40, CD30, CD15), CD3, combined CD20/CD14 and a cell membrane permeability viability dye. The assay was tested using the KMH2 Hodgkin lymphoma cell line spiked into PBMC and transferred to well slides for imaging by CyteFinder. This instrument utilizes 6-color scanning microscopy coupled with predefined algorithms to identify rare cell populations. The assay was then applied to a frozen fine needle aspirate (FNA) sample taken from the lymph node of a patient with histologically confirmed CHL. The FNA sample was thawed, prepared into a suspension, stained and analyzed as above. Cells identified with HRS phenotype were individually retrieved using the integrated CytePicker module. PCR of framework regions of the immunoglobulin heavy chain gene (IGH) was performed on single HRS cells (InvivoScribe) to assess clonality.

Results: Of ~200 KMH2 cells spiked into blood, the assay identified 180 cells (90%) with the correct HRS phenotype. HRS phenotype cells were identified in the patient lymph node FNA sample. Two individual cells analyzed by IGH framework region PCR demonstrated identical size PCR products, indicating clonality of the B cell receptor rearrangement.

Conclusion: A multi-parameter assay was successfully developed for identifying rare HRS cells with the CyteFinder system. Cells with HRS phenotype in a lymph node FNA sample were demonstrated to have clonal IGH rearrangements, demonstrating that actual HRS cells were identified. This method may be a useful tool for the diagnosis of CHL by identification of rare HRS cells from FNA specimens, as well as to investigate the molecular genomics of CHL.

Citation Format: Lance U'Ren, David Wu, Jonathan R. Fromm, Jackie Stilwell, Eric Kaldjian. A multi-parameter assay for the detection of rare malignant cells in classical Hodgkin lymphoma [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 2716. doi:10.1158/1538-7445.AM2017-2716
Abstract 2719: Accelerated BRAF mutation analysis using a fully automated PCR platform improves the management of patients with metastatic melanoma : MELFAST trial
Authors: Harlé Alexandre , Serre Delphine , Salleron Julia , Husson Marie , Leroux Agnès , Geoffrois Lionnel , Merlin Jean-Louis
Published: July 2017

Background : Molecular diagnosis has become a standard of care in many cancers and BRAF mutations analysis in FFPE tumor specimens is needed to initiate personalized therapy using BRAF tyrosine kinase inhibitor (vemurafenib, dabrafenib) in BRAF-mutated metastatic melanoma. Accelerated BRAF mutation analysis is achievable using CE-IVD fully automated (FA) PCR-based platform (Idylla, Biocartis) and enables the determination of BRAF mutational status in less than 2 hours including sample preparation and proved suitable for routine molecular diagnosis of metastatic melanoma (Harlé et al. PloS ONE 11(4); e0153576).

Patients and methods : MELFAST trial is an observational monocentric study aiming at evaluating the clinical impact of reducing BRAF status determination delay in patients with metastatic melanoma. 40 patients (pts) were included in MELFAST trial, 31 pts were included retrospectively with BRAF mutation analysis being performed according to standard operating procedures (SOP) using conventional PCR, 10 pts were included prospectively with BRAF mutation analysis being performed using FA-PCR.

Results : Among the 40 pts included, 3 pts were excluded because of violation of inclusion criteria. 37 pts that were analyzed (29 pts with retrospective inclusion and 8 pts with prospective inclusion). BRAF mutational status was not known at the time of treatment decision in 11/29 (38%) pts included retrospectively and in all the pts included prospectively. Using FA-PCR enables to provide BRAF mutational status within the same day for most of the samples and the reporting delay was significantly reduced using FA-PCR as compared to SOP (0 vs 7 days, p<0.001) and the delay of initiation of anti-BRAF therapy was subsequently reduced (16 vs 26 days, p=0.035). This reduced delay was found to be consistent with that observed when BRAF mutational status had been anticipated and was already available at the time of treatment line decision (20 days, p=0.798).

Conclusion: As compared to conventional SOP, using FA-PCR accelerates BRAF mutation analysis reporting and significantly reduces the delay before initiation of personalized therapy in pts with metastatic melanoma. This warrants the investigation of the impact on the patients outcome i.e. progression free and overall survival.

Citation Format: Alexandre Harlé, Delphine Serre, Julia Salleron, Marie Husson, Agnès Leroux, Lionnel Geoffrois, Jean-Louis Merlin. Accelerated BRAF mutation analysis using a fully automated PCR platform improves the management of patients with metastatic melanoma : MELFAST trial [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 2719. doi:10.1158/1538-7445.AM2017-2719
Abstract 2723: MET exon 14 skipping mutations in advanced non-small cell lung cancer (NSCLC) are not associated with MET amplification and overexpression
Authors: Gimenez-Capitan Ana , Teixidó Cristina , Aguado Cristina , Rodríguez Sonia , Bertran-Alamillo Jordi , Castellví Josep , Yeste Zaira , Pérez Ana , Rosell Rafael , Molina-Vila Miguel Angel
Published: July 2017

Background: Activating alterations of the mesenchymal epithelial transition (MET) oncogene in NSCLC are potentially actionable with targeted MET inhibitors. MET exon 14 skipping mutations have been described in 3% of patients (p) in NSCLC,.Fluorescent in situ hybridization (FISH) and immunohistochemistry (IHC) are currently used for detecting MET amplification and overexpression, respectively, but are not useful to detect MET splicing variants. On the other hand, the reverse transcription-polymerase chain reaction (RT-PCR) technique has the potential to detect this actionable alteration.

Methods: We designed and validated a custom set of 5´and 3´ primers to detect the MET exon 14 splicing variant by RT-PCR. RNA isolation from FFPE samples was performed with Roche High Pure FFPET RNA isolation kit and M-MLV Reverse Transcriptase enzyme was used in the RT-PCR. A panel of cell lines was initially employed to assess the performance of the technique. Subsequently, a total of 232 formalin-fixed paraffin-embedded (FFPE) samples from advanced NSCLC patients were analyzed. Of them, 15 were positive by RT-PCR (n=209) for the MET exon 14 variant. The bands corresponding to the splicing variant were submitted to Sanger sequencing.

Results were compared with FISH (ZytoVision Dual Color probe Z-2087-200) and IHC (Ventana CONFIRM anti-Total c-MET (SP44)). Results: A total of 232 EGFR-wt advanced NSCLC p were analyzed by IHC and 42 (18.1%) were considered as positive (cut-off 3+≥ 50%). Regarding FISH, MET amplification was detected in 13 out of 58 p (22.4%) evaluable while the MET exon 14 skipping variant was detected in 15 (7.2%) out of 209 p . Unexpectedly, only three (21.4%) of the positive MET exon 14 skipping p by RT-PCR were positive for IHC. Finally, of the 15 MET exon 14 positive p, 5 were evaluable for FISH and none of them were positive for MET amplification.

Conclusion: In our cohort of 232 EGFR-wt, advanced NSCLC p, the MET exon 14 skipping mutation had an incidence of 7.2% No correlation was found between the presence of the MET exon 14 variant by RT-PCR and MET overexpression or amplification. Detection of MET exon 14 alterations poses a challenge for diagnostic testing.

Citation Format: Ana Gimenez-Capitan, Cristina Teixidó, Cristina Aguado, Sonia Rodríguez, Jordi Bertran-Alamillo, Josep Castellví, Zaira Yeste, Ana Pérez, Rafael Rosell, Miguel Angel Molina-Vila. MET exon 14 skipping mutations in advanced non-small cell lung cancer (NSCLC) are not associated with MET amplification and overexpression [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 2723. doi:10.1158/1538-7445.AM2017-2723
Abstract 2740: High-throughput and sensitive quantification of circulating tumor DNA
Authors: Guan Yinghui , Mayba Oleg , Lu Shan , Sandmann Thomas , Choi Younjeong , Darbonne Walter , Leveque Vincent , Ryner Lisa , Humke Eric , Tam Nga W. , Sujathasarma Sundari , Cheung Anna , Bourgon Richard , Wang Yulei
Published: July 2017

Circulating tumor DNA (ctDNA) has a great potential to serve as non-invasive biomarkers for monitoring disease progression and treatment response. However, its broad clinical applications have been hindered by sensitivity, throughput and complexity of existing ctDNA detection methods. Here we report an adaptation of a multiplex PCR pre-amplification (PreAmp) into the microfluidic multiplex PCR (MMP-Seq) technology for high-throughput and sensitive quantitation of ctDNA. We have demonstrated that PreAmp MMP-Seq enabled sensitive (down to 0.6% allele frequency), reproducible (R2=0.97), accurate and quantitative mutation detection from as low as 1.6 ng DNA input. An Empirical Bayesian Model has been established to estimate background error rates for every base of amplicons in the ctDNA panel using data from 43 normal plasmas. 0.1-0.3% of median error rates were observed across all positions. 149 longitudinal plasma samples from 12 ovarian and 10 pancreatic cancer patients of PhI DMUC5754A anti-MUC16 ADC trials were then profiled using PreAmp MMP-Seq. 79% (11/14) driver mutations found in tissue samples were also identified in matching baseline plasma samples at frequencies well above estimated error rates. Moreover, we found that changes of corresponding ctDNA concentration in post-treatment plasma samples were correlated with changes in tumor burdens and circulating protein marker levels. In conclusion, the MMP-seq PreAmp workflow provides an inexpensive, reproducible and flexible solution for mutation detection in plasma DNA samples.

Citation Format: Yinghui Guan, Oleg Mayba, Shan Lu, Thomas Sandmann, Younjeong Choi, Walter Darbonne, Vincent Leveque, Lisa Ryner, Eric Humke, Nga W. Tam, Sundari Sujathasarma, Anna Cheung, Richard Bourgon, Yulei Wang. High-throughput and sensitive quantification of 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 2740. doi:10.1158/1538-7445.AM2017-2740
Abstract 2742: Cross-platform comparison of four leading technologies for detecting EGFR mutations in circulating tumor DNA from plasma of patients with non-small cell lung carcinoma
Authors: Xu Ting , Kang Xiaozheng , You Xiaofang , Liang Dai , Tian Dequan , Yan Wanpu , Yang Yongbo , Xiong Hongchao , Liang Zhen , Zhao Grace Q. , Lin Shengrong , Chen Ke-Neng , Xu Guobing
Published: July 2017

Analysis of circulating tumor DNA (ctDNA) is emerging as a powerful tool for guiding targeted therapy and monitoring tumor evolution in patients with non-small cell lung cancer (NSCLC), particularly when fresh tissue biopsy is not available. This study compared the ability of four leading technology platforms to detect epidermal growth factor receptor (EGFR) mutations (L858R, exon 19 deletion, T790M and G719X) in ctDNA from NSCLC patients. The platforms included two amplification refractory mutation systems (cobas-ARMS and ADx-ARMS), a droplet digital polymerase chain reaction platform (ddPCR) and a next-generation sequencing platform (Firefly NGS). Fifteen EGFR mutations across twenty NSCLC patients were identified. We observed superior sensitivity and specificity of cobas-ARMS, ddPCR and Firefly NGS platforms, while ADx-ARMS was only suitable for the qualitative detection of EGFR mutations with allele frequency higher than 1% in plasma samples. We observed high concordance between the plasma and tissue EGFR mutational profiles for three driver mutations that are known targets of the first generation EGFR-TKI therapy (L858R, E19-dels, and G719X). Discrepancies between plasma and tissue EGFR mutational profiling could be attributed to spatial and temporal tumor heterogeneity. This pilot study illustrates the promise of ctDNA analysis in the context of treatment evaluation and drug resistance detection, and results will be validated in follow-up studies.

Citation Format: Ting Xu, Xiaozheng Kang, Xiaofang You, Dai Liang, Dequan Tian, Wanpu Yan, Yongbo Yang, Hongchao Xiong, Zhen Liang, Grace Q. Zhao, Shengrong Lin, Ke-Neng Chen, Guobing Xu. Cross-platform comparison of four leading technologies for detecting EGFR mutations in circulating tumor DNA from plasma of patients with non-small cell lung carcinoma [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 2742. doi:10.1158/1538-7445.AM2017-2742
Abstract 2747: Plasma DNA methylation marker and hepatocellular carcinoma risk prediction model for the general population
Authors: Wu Hui-Chen , Yang Hwai-I , Wang Qiao , Chen Chien-Jen , Santella Regina M.
Published: July 2017

Metastases in the later stages of hepatocellular carcinoma (HCC) cause the majority of deaths associated with the disease, making early detection crucial to patient survival. Risk models that assess HCC risk in the general population can be used for risk stratification for further HCC surveillance, however, none have been validated externally. Methylation of circulating DNA shows potential for noninvasive and early diagnosis of HCC. Most evidence, however, comes from cross-sectional studies raising concerns about temporality. We conducted a prospective case-control study nested within a community-based cohort. We measured methylation levels in of 6 genes (CDKN2A, RASSF1A, STEAP4, TBX2, VIM, and ZNF154) using pre-diagnostic plasma DNA from 237 HCC cases and 257 matched controls. We found TBX2 hypermethylation was associated with increased HCC risk, with ORs (95%CI) of 3.7 (1.9-7.2). The associations were mainly among high-risk subjects; among subjects infected with HBV/HCV, the OR (95%CI) of TBX2 methylation was 5.3 (2.2-12.7). Among subjects with high risk, the ORs (95%CIs) were 8.9 (1.0-73.9) for Wen-HCC score ≥16, 5.6 (2.1-14.6) for Hung-HCC score ≥15, and 7.2 (2.1-24.4) for Michikawa-HCC ≥8. Adding information on TBX2 methylation improved the accuracy of risk models for a high risk population, with the area under the curve (AUC) of 74% for TBX2 methylation and Wen-HCC score compared with 64% with Wen-HCC score alone. The AUCs were 63% for Hung-HCC score and TBX2 methylation, 53% for Hung-HCC score alone, 65% for Michikawa-HCC score and TBX2 methylation and 59% for Michikawa-HCC risk alone. Our findings suggest the potential increase in risk assessment discrimination and accuracy from incorporation of DNA methylation.

Citation Format: Hui-Chen Wu, Hwai-I Yang, Qiao Wang, Chien-Jen Chen, Regina M. Santella. Plasma DNA methylation marker and hepatocellular carcinoma risk prediction model for the general population [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 2747. doi:10.1158/1538-7445.AM2017-2747
Abstract 2748: Liquid biopsy using extracellular vesicular DNA for EGFR mutation testing in the patients with NSCLC
Authors: Hur Jae Young , Kim Hee Jung , Choi Chang-Min , Lee Jae Cheol , Lee Kye Young
Published: July 2017

Background Tumor-derived extracelluar vesicles (EV) have been proved to carry double-stranded DNA including oncogenic mutants and expected to be a novel biomarker in cancer detection. Liquid biopsy using cell-free (cf) DNA for EGFR mutation testing is being actively investigated. In this study, we investigated whether liquid biopsy using EV DNA is superior to cf DNA for EGFR mutation testing in the patients with NSCLC.

Methods EV was isolated using ultracentrifugation and confirmed by transmission electron microscopy and zetasizer in 20 plasma samples (all tissue-proven EGFR mutated) and 32 bronchoalveolar lavage fluid (BALF) samples (23 EGFR-mutated including 14 TKI-naïve and 9 TKI resistant, and 9 wild-type). EV and cf DNA was separately extracted from each samples and EGFR mutation testing was performed by peptide nucleic acid (PNA)-clamping method.

Results In 20 plasma samples, the concordance rate of EV DNA for tissue EGFR genotyping was 55% (11/20), while 30% (6/20) in cf DNA. In 32 BALF samples, however, the sensitivity, specificity and concordance rate of EV DNA for activating EGFR mutations was 100% (23/23), 100% (9/9), and 100% (32/32), while cf DNA showed 73.9% (17/23), 100% (9/9) and 81.3% (26/32), respectively. The kappa value (p-value) of EV DNA was 1.0 (<0.001), while it was 0.714 (p,0.001) in the case of cf DNA. As for 9 re-biopsy cases for T790M detection in which only 3 patients (33%) was proved as positive T790M, BALF EV DNA identified 2 more T790M patients (total 5 among 9 patients, 56%) without non-matching with tissue typing, while BALF cf DNA found 1 more T790M positive patient with missing 1 tissue proven case (total 3 among 9 patients, 33%)

Conclusions Liquid biopsy using EV DNA is significantly superior to cf DNA in both plasma and BALF. A little low sensitivity in plasma EV DNA is supposed to be improved with much more sensitive method such as ddPCR or BEAMing. Liquid biopsy using BALF EV DNA showed almost 100% matching with tissue EGFR typing and seems to be highly promising for T790M detection. A large number of clinical trials should be prompted.

Citation Format: Jae Young Hur, Hee Jung Kim, Chang-Min Choi, Jae Cheol Lee, Kye Young Lee. Liquid biopsy using extracellular vesicular DNA for EGFR mutation testing in the patients with NSCLC [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 2748. doi:10.1158/1538-7445.AM2017-2748
Abstract 2759: Technical limitations of capture-based, targeted deep sequencing for the detection of somatic variations in cell-free DNA
Authors: Park Gahee
Published: July 2017

Despite widespread applications of capture-based targeted deep sequencing, its limitations on detecting circulating tumor DNA (ctDNA) have not been systematically elucidated. Here, we analyze and characterize parameters critically determining its detection limits; depth of coverage and background errors. The depth increase by using more cell-free DNA (cfDNA) was saturated at around ~3000x with ~50 ng of cfDNA primarily due to a deduplication artifact, which limited the detection sensitivity of the method. Next, characterizing background errors, we uncovered that a majority of errors were not derived from biological origins but technical artifacts, especially during sample preparation and library construction rather than sequencing. Thus, it is important to use an appropriate protocol for those steps minimizing background errors. Considering the depth of coverage and the background error rate, we estimated the detection limit of the method approximately to be 0.4% variant allele frequency at 95% confidence level. Applying the method to pancreatic cancer patients, we found that the levels of ctDNAs measured by cfDNA sequencing well correlated with clinical responses to therapy and/or disease progression, but biopsy-free profiling of somatic variants was limited by the moderate sensitivity of 72% and PPV of 74% at the variant level. Our results clarify technical limitations of targeted deep sequencing and provide a guideline for applying the technique to analyze cfDNA.

Citation Format: Gahee Park. Technical limitations of capture-based, targeted deep sequencing for the detection of somatic variations in cell-free 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 2759. doi:10.1158/1538-7445.AM2017-2759
Abstract 276: Retrospective analysis of epidemiological variants of malignancies in Sokoto, Northwestern Nigeria
Authors: Sahabi Saddiku M. , Abdullahi Kabiru
Published: July 2017

Background: The burden of cancer in Nigeria is increasing. Information on incidence, prevalence, pattern, and high risk factors are essential for evaluation and cancer control. This report is a follow up from earlier previous report published in 2005 on cancers seen in Usmanu Danfodiyo University Teaching Hospital (UDUTH) Sokoto.

Objectives: The aim of this study is to determine epidemiological variants of all malignancies seen from 1 January 2006 to 31 December 2015.

Materials and Methods: This is a retrospective review of all malignancies seen at the Usmanu Danfodiyo University Teaching Hospital in Sokoto during the period 2006 to 2016. There was no restriction on gender or age groups. Mean, frequencies, percentages, and independent sample t-test were performed using SPSS version 21.0 for Windows. Significant level set at p < 0.05.

Results: A total of 3933 cancer patients were seen during the ten-year period. There were more female malignancies (n=2260, 57.5%) compared to male malignancies (n=1673, 42.5%). The overall mean age (years) was 44.28, median age was 45.0, modal age was 50, and SD was 18.69; the age range was 1 to 99 years. Males (mean age 45.77, median age in male 50.0, modal age 60, and SD 21.03) were significantly older than females (mean age 43.18, median age 45.0, modal age 50, and SD 16.67). The adult malignancies account for 90.9% (n=3575) and childhood malignancies account for 9.1% (n=358). Overall, the ten most common malignancies were: breast 763 (19.4%), cervix 312 (7.9%), prostate 267 (6.8%), lymph node 248 (6.3%), skin 225 (5.7%), bladder 191 (4.9%), rectum 114 (2.9%), ovary 110 (2.8%), eye 97 (2.5%), soft tissue 95 (2.4%). In males, the ten most frequent malignancies were: prostate 267 (16.00%), bladder 160 (9.60%), skin 138 (8.20%), nasophraynx 87 (5.2%), lymph node 85 (5.10%), rectum 61 (3.60%), eye 55 (3.30%), salivary gland 38 (2.3%), larynx 37 (2.20%), and anal 37 (2.20%). In females, the ten most common malignancies were breast 731 (731%), cervix 302 (13.40%), lymph node 163 (7.20%), ovary 110 (4.90%), skin 87 (3.80%) endometrial 61 (2.70%), rectum 53 (2.30%), nasophraynx 45 (2.0%), soft tissue 43 (1.90%), and eye 42 (1.90%).

Conclusion: Our study concludes that malignancies of the breast, cervix, and prostate are the three most common in our environment. These malignancies tend to present at younger age (less than 50 years of age) compared to other developing countries. Therefore, public education and well developed screening programs are urgently needed to overcome this burden.

Citation Format: Saddiku M. Sahabi, Kabiru Abdullahi. Retrospective analysis of epidemiological variants of malignancies in Sokoto, Northwestern Nigeria [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 276. doi:10.1158/1538-7445.AM2017-276
Abstract 2780: High nuclear FTH1 protein expression predicts early disease recurrence for BRCA1/2 mutation carriers
Authors: Hollestelle Antoinette , Timmermans Mieke , Broeren-Foekens Renée , Jansen Anita Trapman - , Deurzen Carolien H. van , Umar Arzu , Martens John W. , Hooning Maartje
Published: July 2017

FTH1 is a 21kD subunit of the ferritin complex, which is involved in intracellular iron storage. In a previous study we found that FTH1 proteins can be located either in the cytoplasm or nucleus and, depending on its cellular localization, is associated with good or poor prognosis in triple negative breast cancer (TNBC). Furthermore, cytoplasmic localization of cFTH1 was associated with an increased anti-tumor (CD8+) T-cell / tumor-promoting (CD4+) T-cell ratio suggesting an immune modulatory role for FTH1. In the current study we have assessed the prognostic value of FTH1 expression for BRCA1/2 mutation carriers. FTH1 proteins were visualized by immunohistochemistry on a tissue microarray containing primary breast cancer specimens from 222 BRCA1/2 mutation carriers that were diagnosed between 1982 and 2008. Primary breast cancers from BRCA1 carriers were predominantly of the TNBC subtype, whereas primary breast cancers from BRCA2 mutation carriers were mainly ER-positive. The association between FTH1 expression and clinical outcome was evaluated by a Cox proportional hazards regression model using left truncation to adjust for study inclusion bias. The median follow-up time of the study was 9.2 years. High nuclear FTH1 (nFTH1), but not cytoplasmic FTH1 (cFTH1), was associated with decreased metastasis-free and disease-free survival as compared with low nFTH1 (multivariable HR=3.54, 95% CI=1.45-8.66, P=0.0056 adjusted for tumor size and nodal status; multivariable HR=2.71, 95% CI=1.49-4.92, P=0.0011 adjusted for tumor size). Neither nFTH1 nor cFTH1 were associated with breast cancer-specific or overall survival. This suggests that high nFTH1 expression in primary breast cancer predicts earlier disease recurrence for BRCA1/2 mutation carriers. Since we had observed that CD4+:CD8+ T-cell ratios were increased among TNBCs with high nFTH1, we hypothesize that nFTH1 promotes recruitment of immune suppressive CD4+/FOXP3+ regulatory T-cells in TNBC and BRCA1/2-associated tumors, suppressing CD4+/FOXP3- and CD8+ T-cell anti-tumor immunity.

Citation Format: Antoinette Hollestelle, Mieke Timmermans, Renée Broeren-Foekens, Anita Trapman - Jansen, Carolien H. van Deurzen, Arzu Umar, John W. Martens, Maartje Hooning. High nuclear FTH1 protein expression predicts early disease recurrence for BRCA1/2 mutation carriers [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 2780. doi:10.1158/1538-7445.AM2017-2780
Abstract 2784: Identifying biomarkers to predict cardiotoxicity of doxorubicin in individual patients
Authors: Zhao Liqun , Zhang Baolin
Published: July 2017

Doxorubicin is a highly effective anticancer agent but causes cardiotoxicity in many patients. This study aims to identify biomarkers to predict potential cardiotoxicity before the onset of cardiac tissue damage and dysfunction in individual cancer patients. First, we established a human cellular system to model the cardiac toxicity of oncology drugs using human induced pluripotent stem cells-derived cardiomyocytes (iPS-CMs). We tested a panel of clinically used drugs including anthracyclines (doxorubicin, daunorubicin, epirubicin and idarubicin), 5-FU, Taxol, Trastuzumab, and tyrosine kinase inhibitors (sunitinb, imatinib, and sorafinib). These drugs displayed varying degrees of cytotoxicity in iPS-CMs which are generally consistent with their known cardiotoxicity patterns. Second, we found that doxorubicin selectively upregulated the expression of death receptors in iPS-CMs. As a result, the treated iPS-CMs underwent spontaneous apoptosis that was further enhanced in the presence of specific cytokines. Based on these findings, we hypothesize that the baseline levels of the predefined cytokines in blood could be predictive of cardiotoxicity associated with doxorubicin treatment in individual patients. We are currently investigating the relationships between the levels of the predefined cytokine signature in blood and cardiac events in patients who received doxorubicin or related anthracycline therapy.

Citation Format: Liqun Zhao, Baolin Zhang. Identifying biomarkers to predict cardiotoxicity of doxorubicin in individual patients [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 2784. doi:10.1158/1538-7445.AM2017-2784