bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2796: Validation of Brightplex, a multiplexed IHC solution for immune cell phenotyping of the tumor microenvironment
Authors: Collignon Aurélie , Benchaaben Assil , Kassambara Alboukadel , Guimaraes Felipe , Prestat Emmanuel , Haond Christophe , Fieschi Jacques 
Published: August 2019

Abstract
Brightplex is a multiplexing solution developed by HalioDx to analyze the tumor microenvironment on FFPE tissue. It leverages chromogenic immunohistochemistry performed by iterative automated immunostaining on the same slide followed by whole slide digital pathology analysis based on proprietary software combined to Halo from Indica Lab. Stained cells can be quantified in various regions of interest (tumor, stroma, invasion margin). The Brightplex T cell exhaustion (TCE) panel includes 5 biomarkers (CD3, CD8, PD1, TIM3 and LAG3) to assess the expression of three immune checkpoints on T cells. This panel is intended to be used in clinical research to identify patients susceptible to respond to new immunotherapies especially in the context of the resistance to anti PD(L)1 treatment. Therefore, it is critical to thoroughly demonstrate the robustness and the accuracy of such complex assay. For the validation study of the TCE panel, tissue sections were sequentially immunostained for TIM3, PD1, LAG3, CD8 and CD3. Following each immunostaining, the slides were digitized, de-stained and the antibodies stripped before the next immunostaining. Images of the whole slide were then coregistered and analyzed by digital pathology to determine the densities of various T cell populations: CD8+ T lymphocytes expressing of 1, 2 or 3 immune checkpoints. The precision of the assay was evaluated in terms of intra- and inter-run repeatability and the accuracy was evaluated by comparison of the automated multiplex assay with singleplex staining. Results demonstrate the reliability of Brightplex to analyze tumor sections. The precision study showed that Brightplex was reproductible on several tumor types such as NSCLC, colon and breast and the accuracy was demonstrated by comparison of cell density for each biomarker following either multiplex or singleplex staining. The high degree of robustness could be explained notably by the iterative chromogenic immunohistochemistry technology which limits the risks of steric hindrance when antibodies and amplification systems are used simultaneously and by the intrinsic robustness of this routine workflow including IVD grade instrument and reagents.
Citation Format: Aurélie Collignon, Assil Benchaaben, Alboukadel Kassambara, Felipe Guimaraes, Emmanuel Prestat, Christophe Haond, Jacques Fieschi. Validation of Brightplex, a multiplexed IHC solution for immune cell phenotyping of the tumor microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2796.
Abstract 2797: Accumulation of neutrophils in the tumor microenvironment promotes resistance to immunotherapy in pancreatic cancer
Authors: Siolas Despina , Vucic Emily , Cullis Jane , Choi Mark , Bar-Sagi Dafna 
Published: August 2019

Abstract
The prognosis for pancreatic cancer patients is unequivocally poor. This is due in part to the fibrotic and immunosuppressive microenvironment of pancreatic tumors, which serves as a physical barrier to chemotherapy and immunotherapy. Intratumoral genetic alterations can cause remodeling of the immune environment through distinct cellular mechanisms. Oncogenic Kras gene mutations are the most frequently occurring genetic event in pancreatic cancer, followed by transforming alterations in TP53. We show that CRISPR/Cas engineered KrasG12D;Trp53R172H pancreatic ductal tumors have a distinct immune profile characterized by an increase in neutrophils and a concomitant decrease in cytotoxic and Th1+ T cells. In addition, KrasG12D;Trp53R172H pancreatic ductal tumors have an increase in CXCL5, a chemokine involved in neutrophil accumulation. Analysis of publicly available datasets shows that increased neutrophil numbers significantly correlate with decreased survival in pancreatic cancer patients. Of clinical relevance, p53-Crispr/Cas engineered pancreatic tumors in mice are resistant to immunotherapy/chemotherapy combination treatment. This data supports the possibility of personalizing immunotherapy treatments based on immune profiles.
Citation Format: Despina Siolas, Emily Vucic, Jane Cullis, Mark Choi, Dafna Bar-Sagi. Accumulation of neutrophils in the tumor microenvironment promotes resistance to immunotherapy in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2797.
Abstract 2831: Detection of methane-producing archaea in the cervix of Hispanics using shotgun metagenomics
Authors: Godoy-Vitorino Filipa , Vazquez-Sanchez Frances , Dominicci-Maura Anelisse , Romaguera Josefina 
Published: August 2019

Abstract
The human cervix is colonized by microbial communities that have traditionally been regarded as a protective barrier against infections. Dysbioses disrupting the balance of the normal microbiota, leads to the appearance of anaerobic taxa that have been related to sexual transmitted infections and cancer. The complexity of the diversity and composition of cervicovaginal communities has been recently highlighted by 16S rDNA surveys, although these have limitations to either select mostly bacteria and the lack of strong lower taxonomic resolution such as being species-specific. Metagenomic shotgun sequencing overcomes these limitations, and gives us access to the extent of diversity beyond bacterial communities. This is the first project to characterize the bacterial and archaeal communities of the cervix of Puerto Ricans using shotgun metagenomics. Women coming for gynecology and colposcopy evaluation at the UPR and San Juan City clinics (San Juan Metropolitan area), and who did not meet several excluding criteria including having taken antibiotics for the last month, were recruited for the study. Samples were acquired by inserting a speculum for access and visualization of the cervix and a sterile swab was rotated along the lumen with a circular motion and frozen immediately for posterior genomic DNA extractions and sequencing. Library construction and shotgun sequencing of 10 cervical patient samples was done with the Illumina HiSeq platform An average of 1,690,000 good quality reads per sample were analyzed. Approximately 90% of the contigs had more than 1,000bp and 10% had sizes ranging from 1,000-5,000bp. Microbial communities were dominated by Lactobacillus, including L. iners, Gardnerella vaginallis, Nocardia and Atapobium vaginae. Archaeal diversity was dominated by Methanosarcina (namely, M. barkeri) with other less dominant taxa such as Methanolobus, Methanococcus, Natrococcus and Methanobrevibacter. The dominance of Lactobacillus was expected, and as Archaea are environmental organisms that have been associated with the mucosa in mammals, including protecting the human gut, they must have an important role in the cervix. As methanogenic archaea are known to remove fermentation end products, such as methanol and ethanol, as end-products of other fermentative bacteria, methanogenesis maybe important in preventing the accumulation of gases and other reaction end products that could damage the cervical mucosa.
Citation Format: Filipa Godoy-Vitorino, Frances Vazquez-Sanchez, Anelisse Dominicci-Maura, Josefina Romaguera. Detection of methane-producing archaea in the cervix of Hispanics using shotgun metagenomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2831.
Abstract 2839: Leveraging gut microbiota networks to impact tumor immunotherapy
Authors: Jayaraman Lata , Sceneay Jaclyn 
Published: August 2019

Abstract
The human gut microbiota forms a diverse, dynamic and complex ecosystem that modulates numerous host processes including metabolism, inflammation and cellular and humoral immune responses. Emerging data suggest that the gut microbiota of cancer patients may predict tumor response to immune checkpoint inhibitors (ICI). To better understand how the microbiome may impact response to ICI, we have developed and validated robust tumor models using either conventional mice treated with antibiotics or germ-free (GF) mice. We have confirmed in both models, that mice lacking a diverse microbiome fail to mount an efficient anti-tumor immune response after treatment with anti-PD-1, primarily due to T cell dysfunction. This response to anti-PD-1 can be restored by introduction of a microbiome using fecal microbial transplant (FMT) prepared from stool from healthy donors in GF mice, and is driven by increased tumor-infiltrating lymphocytes (TILs), specifically CD8+ T cells. Importantly, for the first time, we show that the bacterial spore fraction from healthy donor stool can also restore response to anti-PD-1 and increase CD8+ TILs in both conventional mice treated with antibiotics and GF mice. We have also tested cancer patient-derived microbiome samples that are efficacious or non-efficacious in GF mouse models. We have sequenced the input material as well as the engrafted gut microbiota in these mice via 16S rDNA sequencing. Comparison of these sequences has enabled us to develop a “microbiome signature” of response that is being used in the development of a microbiome-based therapy for combination with ICI. Based on these encouraging animal model data we plan to initiate a randomized, placebo-controlled clinical study in patients with advanced metastatic melanoma. The clinical trial will evaluate the impact of an anti-PD-1 checkpoint inhibitor with adjunctive microbiome therapy on patient outcomes. Seres is developing SER-401, a preclinical stage oral microbiome therapy to improve the efficacy and safety of immunotherapy. Our drug discovery strategy combines computational analyses and empirical in vitro, in vivo and ex-vivo screening of strains and consortia to inform selection and drive microbiome drug design. Data from such a comprehensive approach are invaluable for designing compositions of bacteria that form “functional ecological networks” that can impact response to ICI therapy. We believe these data will provide insight into how microbiome drugs can be developed in the setting of immunotherapy to augment the efficacy of ICIs by altering the cancer-immune set point.
Citation Format: Lata Jayaraman, Jaclyn Sceneay. Leveraging gut microbiota networks to impact tumor immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2839.
Abstract 2842: Vesal Yaghoobi
Authors: Yaghoobi Vesal , Pelekanou Vasiliki , O'Meara Tess , Silber Andrea , Pusztai Lajos , Rimm David 
Published: August 2019

Abstract
Background: It has been shown that even after adjusting for clinical stage at presentation and socio-economic variables, Triple Negative Breast Cancer (TNBC) still has a worse overall outcome in African American (AA) compared to Non-African American (NAA) patients. The abundance and composition of immune cells in the tumor microenvironment is a powerful prognostic factor in TNBC. Our goal was to assess if differences exist in CD8, CD68 and PD-L1 protein expression between AA and NAA TNBC. We hypothesize that the microenvironment of African AA TNBC patients may be different than that of NAAs.
Method: We selected N=43 AA and N=43 NAA TNBC samples from the Yale Pathology archives that were matched by diagnosis date. We measured CD8, CD68 and PD-L1 protein expression in both the tumor and stromal compartments in whole slides from formalin fixed paraffin embedded (FFPE) tissues using multiplexed quantitative immunofluorescence (QIF). The average of each marker expression was calculated in all Fields of View (FOV), and the top 10% brightest FOV of each slide (i.e. hotspot).
Results: The frequency of macrophages, as assessed by the expression of CD68 was significantly higher in AA compared to NAA. This was seen by overall assessment for all FOV (mean NAA=2273au versus mean AA=3627au; p = 0.0052), and in hotspot FOVs (mean NAA=4858au versus mean AA=6371au; p = 0.0411), and also for assessments in tumor and stromal subcompartments. Expression of CD8 positive cytotoxic T cells was significantly lower in AA compared to NAA, but only when measuring hotspots in the tumor compartment (p=0.017).
Conclusion: The significantly higher CD68 and lower CD8 expression in AA compared to NAA TNBC might contribute to a more immune attenuated microenvironment. We are currently further characterizing the macrophage polarity and the cytokine milieu of these samples.
Citation Format: Vesal Yaghoobi, Vasiliki Pelekanou, Tess O'Meara, Andrea Silber, Lajos Pusztai, David Rimm. Vesal Yaghoobi [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2842.
Abstract 2848: TSPAN8-EPS8L3 signaling play a role in EGF-dependent pancreatic cancer cell invasion and migration
Authors: Li Junjian , Zhu Rongxuan , Ju Gaoda , Ge Weiyu , Jiang Mengyi , Zhou Tianhao , Wang Hongxia 
Published: August 2019

Abstract
The mechanism and function of TSPAN8 on the invasion and metastasis of cancer cells is poorly understood. In present study, we demonstrated that TSPAN8 over-expressed in pancreatic cancer (Paca) tissues (37.98%) comparing with normal tissue (0%). TSPAN8 expression levels were reversely correlated with the overall survival time of Paca patients (p = 0.021). In vitro, over-expressed or knockdown TSPAN8 expression in Paca cells SW1990 or Capan-2 and AsPC-1 modulated invasion, immigration and clone formation ability. Mechanistically, we revealed that SOX9, a downstream transcription factor of EGFR signaling, activated TSPAN8 transcription under EGF condition. Meanwhile, we uncovered a previously uncharacterized mechanism underlying EGF-dependent Paca cells invasion and migration. In brief, TSPAN8 was phosphorylated at Ser129 by AKT, resulting in the binding of TSPAN8 with BCAFL1, TSPAN8 entering nucleus and regulating the EPS8L3 transcription, remodeling of cytoskeleton, and enhancing cell invasion and migration. By single cell seq analysis of Paca cells derived from patients and tissue array assay, we validated that the EGFR and EPS8L3 expression in mRNA and protein level were highly correlated with TSPAN8 expression. In vivo and in vitro study demonstrated that EPS8L3 depletion or overexpression rescued the invasion ability induced by TSPAN8. These findings reveal a molecular basis of EGF-TSPAN8-EPS8L3 signaling and highlight the critical role of TSPAN8 in tumor metastasis.
Citation Format: Junjian Li, Rongxuan Zhu, Gaoda Ju, Weiyu Ge, Mengyi Jiang, Tianhao Zhou, Hongxia Wang. TSPAN8-EPS8L3 signaling play a role in EGF-dependent pancreatic cancer cell invasion and migration [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2848.
Abstract 2853: Cell motility and invasiveness are promoted by guanylate binding protein 1, GBP-1 in lung adenocarcinoma
Authors: Mimae Takahiro , Yamakita Ichiko , Tsutani Yasuhiro , Miyata Yoshihiro , Ito Akihiko , Okada Morihito 
Published: August 2019

Abstract
Previously, we identified candidate molecules involved in human lung adenocarcinoma progression from non-invasive to invasive tumor by comparing gene expression profiles of each component in the same tumor using laser microdissection and DNA microarray analysis. Among them, guanylate-binding protein 1 (GBP-1) was selected for further analysis because RT-PCR for normal lung and invasive human lung adenocarcinoma tissue samples showed that the relative GBP-1 gene expression levels normalized to GAPDH for invasive lung adenocarcinoma were approximately three-fold higher than those for normal lung samples. In addition, GBP-1 gene and protein expression levels were also higher in mesenchymal-like than in epithelial-like lung cancer cell lines. To determine whether GBP-1 is involved in lung adenocarcinoma cell motility and invasion, we performed migration and wound healing assays using RERF-LC-OK, human lung adenocarcinoma cells transfected with siRNAs. The relative migration of transfected GBP1-siRNA cells was significantly lower than that of control-siRNA cells. The relative wound healing capacities were assessed after scratching. Cells transfected with GBP1-siRNAs were also significantly lower than those of the control-siRNAcells. Moreover, Immunohistochemistry of 80 patients with stage I lung adenocarcinoma demonstrated that non-invasive component cells showed clearly negative GBP-1 expression in all cases. On the other hand, invasive component cells were GBP-1 positive in 10 cases (12.5%) and GBP-1 negative in 70 cases (87.5%). Lymphatic-vascular invasion was positive in 20 patients (25%) and positively correlated with GBP-1 expression (P&lt; 0.05). In conclusion, GBP-1 might enhance lung adenocarcinoma cell motility and invasiveness and controlling of GBP-1 expression has the potential to contribute to the development of novel therapeutic strategies for lung adenocarcinoma.
Citation Format: Takahiro Mimae, Ichiko Yamakita, Yasuhiro Tsutani, Yoshihiro Miyata, Akihiko Ito, Morihito Okada. Cell motility and invasiveness are promoted by guanylate binding protein 1, GBP-1 in lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2853.
Abstract 2860: RCP augments oral cancer cell invasion through Zeb1 and Slug expression
Authors: Kim Jin Young , Cho Kyung Hwa , Jeong Bo Young , Song Zi Hae , Park Chang Gyo , Lee Hoi Young 
Published: August 2019

Abstract
Background: Rab coupling protein (RCP), also called family interacting protein 1 (Rab11fip1) is a protein encoded by the RAB11FIP1 gene and has been known to augment cancer tumorigenesis, invasion, and metastasis. Recently, RCP was reported to aggravate cancer cell invasion and metastasis by stabilizing beta1 integrin and inducing epithelial-mesenchymal transition (EMT) in breast and ovarian cancer. Further, a high RCP expression was significantly correlated with shorter overall survival and disease-free survival of HNSCC patients. However, the molecule mechanisms by which RCP increases HNSCC invasion and metastasis are unclear. In the present study, we demonstrate the role of RCP in oral cancer cell invasiveness and its underlying mechanism.
Methods: Oral cancer YD-10B and YD-38 cells were transiently transfected with RCP constructs. siRNAs were used to analyze the role of specific proteins for Slug and Zeb1 expression. Immunoblotting and immunofluorescence were used to analyze protein expression. Matrigel-coated in vitro insert and wound healing assay were used to analyze cancer cell invasion and migration, respectively.
Results: We observed that ectopic expression of RCP induces invasion of oral cancer cells. Conversely, silencing of RCP expression increased E-cadherin expression and reduced oral cancer cell invasion. In addition, RCP upregulated Zeb1 and Slug expression that is important for RCP-induced oral cancer cell EMT and invasion. Furthermore, we identified that silencing of beta1 integrin efficiently attenuates RCP-induced Zeb1 and Slug expression. In addition, we observed that a selective inhibitor of EGFR kinase activity, Gefitinib, significantly reduces RCP-induced Zeb1 and Slug expression and that RasN17 recovers RCP-induced Zeb1 expression. Finally, RCP increased the viability of oral cancer cells against a chemotherapeutic agent cisplatin.
Conclusion: Collectively, we demonstrate that RCP augments oral cancer cell EMT and invasiveness through a beta1 integrin/EGFR/Ras/Slug and Zeb1 signaling axis, providing potential biomarkers for oral cancer patients therapy.
Citation Format: Jin Young Kim, Kyung Hwa Cho, Bo Young Jeong, Zi Hae Song, Chang Gyo Park, Hoi Young Lee. RCP augments oral cancer cell invasion through Zeb1 and Slug expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2860.
Abstract 2866: Surfaceome profiling in osteosarcoma: Identification of the candidate immunotherapeutic target
Authors: Wang Yifei , Zhang Zhongting , Kannan Sankaranarayanan , Zhang Wendong , Roth Michael , Gill Jonathan B. , Xu Zhaohui , Tian Xiangjun , Wang Jing , Gorlick Richard 
Published: August 2019

Abstract
Osteosarcoma (OS) is the most common primary malignant bone tumor in pediatric patients. Current developments in targeted therapeutic strategies show potential clinical implications in cancer treatments. However, immunotherapies such as antibody-drug conjugates (ADCs) or CAR-T cell therapy have not been sufficiently studied in OS because of the lack of tumor-specific target. In this study, we developed a multi-step RNA-seq based pipeline. First, we did RNA sequencing for our OS PDX models and 17 patient-derived OS cell lines. The results are then pooled with the RNQ-seq data from 111 OS patient via the Therapeutically Applicable Research to Generate Effective Treatments project (TARGET). All these tumor data are subsequently compared with normal tissue RNA-sequencing data from NIH Genotype-Tissue Expression (GTEx) database. The significantly differentially expressed genes (log fold change tumor versus normal &gt;1 for each tissue, p &lt; 0.01) are selected. We further filtered this gene list by cell surface protein prediction based on Gene Ontology, the TransMembrane prediction using hidden Markov models (TMHMM), and glycosylphosphatidylinositol (GPI)-anchored protein annotations. Based on the transcriptomic result, ranks of differentially expressed genes were generated. CD276, LCLAT1, and OR8B12 are the surface markers with high ranks. To validate the transcriptomic results, we prepared surface protein extraction of the PDX models and patient-derived OS cell lines. We are profiling these surface proteins by proteomic mass spectrometry. Further validation for the expression level and location of these markers are underway. Our current finding is not previously reported in OS. The results warrant further development of ADC and car-T cell therapy.
Note: This abstract was not presented at the meeting.
Citation Format: Yifei Wang, Zhongting Zhang, Sankaranarayanan Kannan, Wendong Zhang, Michael Roth, Jonathan B. Gill, Zhaohui Xu, Xiangjun Tian, Jing Wang, Richard Gorlick. Surfaceome profiling in osteosarcoma: Identification of the candidate immunotherapeutic target [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2866.