bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A26: Comparison of DNA extraction kits for metagenomic studies in feces
Authors: Takenaka Isabella Kuniko T. , Moda Bruno S. , Bartelli Thaís F. , Amorim Maria G. , Albuquerque Gabriela E. , Thomas Andrew M. , Dias-Neto Emmanuel , Nunes Diana N. 
Published: December 2020

Abstract
DNA extraction is a critical step in metagenomic studies since it requires the proper lysis of cell walls, allowing the recovery of nucleic acids that would represent the total diversity of communities. Recent studies indicated that the use of different DNA extraction methods in the same sample yielded distinct microbial profiles, highlighting the importance of standardization in DNA extraction methodologies to accurately measure the human microbiome. These issues are even more critical when limiting amounts of samples are available, or when studies target communities with reduced abundance, such as fungi, which represents only 0.1% of total gut microbiota, as has been poorly explored. Here we investigated the performance of three commercial kits for DNA extraction from human fecal samples: QIAamp DNA Stool Mini Kit (Qiagen), E.Z.N.A. Stool DNA Kit (Omega), and ZymoBIOMICS DNA Kit (Zymo), all with or without adding an enzymatic extraction with MetaPolyzyme (MAC4L - Sigma), in an attempt to improve the microbiome community profiling. After extraction, DNA-quality and yield were evaluated using Qubit and real-time PCR, V4-V5 16S rRNA and ITS2 followed by DNA sequencing, as well as further analysis using shotgun DNA sequencing. No significant differences were observed in DNA yield as evaluated by Qubit; an average of 40.3 ng/ul of DNA was obtained for all samples and kits. For both fungi and bacteria analysis, the addition of MAC4L in the extraction protocol apparently did not change the alpha diversity (observed and Shannon) for both individuals. Our analysis for samples extracted with different kits, with or without MAC4L, indicated the percentage of reads from bacteria to vary between 85-90%, whereas fungi were between 0.29-0.49%. Human DNA was also found, as expected, and relative amounts varied from 0.1 to 0.3%. qPCR showed that for all kits up to 50ng of DNA/15uL reaction can be safely used, with no significant DNA polymerase inhibition. These results showed similar efficacy for the three kits in representing bacteria and fungi from feces, and maybe because all these kits had a bead-beading step we had no clear benefits from adding extra enzymatic digestion steps with MAC4L. Finally, we decided to use the Omega kit in our lab, since it combines a simple extraction protocol and is reliable and cost-effective.
Citation Format: Isabella Kuniko T. Takenaka, Bruno S. Moda, Thaís F. Bartelli, Maria G. Amorim, Gabriela E. Albuquerque, Andrew M. Thomas, Emmanuel Dias-Neto, Diana N. Nunes. Comparison of DNA extraction kits for metagenomic studies in feces [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr A26.
Abstract B16: High-resolution metagenomic profiling revealed gut microbiome features for the response to cancer immunotherapy reproducible among multiple cohorts of patients
Authors: Kim Chan Yeong , Ahn Beung-Chul , Hong Min Hee , Chun Yoo Jin , Kim Hye Ryun , Lee Insuk 
Published: December 2020

Abstract
Cancer immunotherapy is currently standard of treatment showing significant clinical benefits to cancer patients, but the beneficial effects are limited to a relatively small subset of patients. Of various factors that may affect the efficacy of cancer immunotherapy, the gut microbiome is receiving more attention because of its strong correlation with immune regulation. Recently, independent studies based on Western populations have identified several taxa that are differentially abundant between responders and nonresponders. However, the reported taxa associated with anti-PD-1 response differ entirely among these studies. In this study, we performed 1) deep (&gt;100M reads in average) metagenome shotgun sequencing on the fecal sample of 49 Korean non-small cell lung cancer (NSCLC) patients, 2) taxonomic profiling using a highly comprehensive gut microbiome-specific genome database, and 3) gene-level profiling with the gut microbiome specific gene catalog to improve the resolution of metagenomic analysis. With the high-resolution metagenomic profiling, we found several taxonomic and functional signatures associated with the response of anti-PD-1 therapy. Interestingly, we found that some of the signatures were reproduced in five independent datasets regardless of the cancer types (melanoma, NSCLC, and renal cell carcinoma) and the type of immunotherapy (anti-PD-1, anti-CTLA4, and the combination of them). For instance, a responder-enriched taxon in the Korean cohort was more frequently detected in the responders in all cohorts (abundance fold-change &gt; 2) and significantly enriched (p&lt;0.05) in two cohorts. Moreover, when we performed an association analysis with the combined profile, the taxon was identified with the highest significance among the differentially abundant taxa (fold-change=2.41, p=2.5e-06). Consistent with the result of the taxon-level analysis, we found that the genes encoded by the taxon were also enriched in responders in multiple studies. In summary, using high-resolution metagenomic profiling, we identified gut microbiome features for the response to cancer immunotherapy shared across multiple cohorts for the first time, to the best of our knowledge.
Citation Format: Chan Yeong Kim, Beung-Chul Ahn, Min Hee Hong, Yoo Jin Chun, Hye Ryun Kim, Insuk Lee. High-resolution metagenomic profiling revealed gut microbiome features for the response to cancer immunotherapy reproducible among multiple cohorts of patients [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr B16.
Abstract IA09: The particulars of circulars: Novel RNAs from oncogenic herpesviruses
Authors: Chang Yuan 
Published: December 2020

Abstract
Circular RNAs (circRNA) are formed by backsplicing of linear RNA. Due to their covalently joined cyclized nature, circRNAs are resistant to exonucleases and therefore comparatively more stable than their linear counterparts. Kaposi sarcoma-associated herpesvirus (KSHV/HHV8) and Epstein-Barr virus (EBV/HHV4) have recently been found by RNA sequencing to generate circular RNAs (circRNAs) in infected tissues and cell lines. These molecules represent a novel class of viral RNA that may have a more sustained functional role than linear transcripts. Initial characterization shows that circRNAs are expressed in infection-associated diseases and can be regulated depending on virus life cycle—although the quantity, localization, cell type, and viral life cycle expression of individual circRNAs vary considerably. Some viral circRNAs are incorporated into viral particles for preformed delivery, suggesting a potential function in early infection.
Citation Format: Yuan Chang. The particulars of circulars: Novel RNAs from oncogenic herpesviruses [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr IA09.
Abstract IA21: Deciphering the human gut microbiome with chemistry
Authors: Balskus Emily P. 
Published: December 2020

Abstract
The human body is colonized by trillions of microorganisms that exert a profound influence on human biology, in part by providing functional capabilities that extend beyond those of host cells. In particular, there is growing evidence linking chemical processes carried out by the human gut microbiome to diseases such as colorectal cancer. However, we still do not understand the vast majority of the molecular mechanisms underlying this phenomenon. Major obstacles faced in surmounting this knowledge gap include the difficulty in linking functions associated with the human gut microbiota to specific microbial enzymes and the challenge of controlling these activities in complex microbial communities. This talk will discuss my lab’s efforts to characterize gut microbial metabolic activities that are linked to colorectal cancer, including a gut microbial genotoxin called colibactin. Gaining a molecular understanding of cancer-associated gut microbial activities will not only help to elucidate the mechanisms by which these organisms contribute to carcinogenesis but should also enable efforts to treat and prevent disease by manipulating this microbial community.
Citation Format: Emily P. Balskus. Deciphering the human gut microbiome with chemistry [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr IA21.
Abstract IA11: Detecting and targeting cellular heterogeneity of the lymphoid blood malignancies
Authors: Wu Catherine J. 
Published: December 2020

Abstract
Multiple lines of evidence have convincingly demonstrated tumor neoantigens as an important class of immunogenic tumor antigens, and have motivated the development of personalized cancer neoantigen targeting approaches. Neoantigens arise from amino acid changes encoded by somatic mutations in the tumor cell and have the potential to bind to and be presented by personal HLA molecules. Because the immune response has the capacity of addressing multiple tumor neoantigens simultaneously, immune-based therapy has a potential for directly address tumor heterogeneity. As a field, we have now successfully moved beyond the first wave proof-of-concept studies that have demonstrated the safety, feasibility and high immunogenicity of these personalized neoantigen-targeting vaccines. An imperative now is to address the challenges of discovering and optimizing the selection of antigens to target, the delivery approach, and extending this promising approach to a broader array of cancer settings.
Citation Format: Catherine J. Wu. Detecting and targeting cellular heterogeneity of the lymphoid blood malignancies [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr IA11.
Abstract IA18: Genomic evolution of brain metastases: Implications for precision medicine
Authors: Brastianos Priscilla K. 
Published: December 2020

Abstract
Brain metastases are clinically devastating. Up to 25% of cancer patients will develop brain metastases and prognosis in this patient population continues to be poor. The vast majority of clinical trials in the US exclude patients with active brain metastases. Our understanding of how intracranial metastases genetically evolve from primary tumors has historically been limited, which has hampered the development of clinical trials for this patient population. In this presentation, I will present our ongoing work on genomic characterization of central nervous system metastases with a comparison to primary tumors and extracranial sites. Intracranial metastases demonstrate branched evolution, whereby the brain metastases and primary tumors share a common genetic ancestor yet both the primary tumor and brain metastasis continue to evolve independently. We also show that comprehensive genomic characterization of brain metastases, coupled with functional validation in mouse models of metastasis, can lead to the discovery of putative drivers of progression and metastasis. Taken together, our data implies that precision medicine approaches based solely on genetic characterization of extracranial sites tumors may miss potential therapeutic targets from which patients with brain metastases might benefit. Importantly, despite genetic heterogeneity between the brain metastases and extracranial sites, there are common clinically actionable genetic alterations across brain metastases of different histologies. We have translated these findings to clinical trials, including an NCI-sponsored cooperative group genomically-guided clinical trial in patients with progressive brain metastases (Alliance A071701).
Citation Format: Priscilla K. Brastianos. Genomic evolution of brain metastases: Implications for precision medicine [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr IA18.
Abstract PO-011: Role of tumor heterogeneity, tumor microenvironment and tumor initiating cell in gastric carcinogenesis from the perspective of development of hypothesis for its clinical application
Authors: Mukherjee Kalyan Kusum , Mukherjee Dattatreya 
Published: December 2020

Abstract
Gastric Cancer (GC) is one of the most malignant type of cancer due to its rapid progression, distant metastasis and resistant to conventional chemotherapy. This study is to search the development towards specific therapy to overcome conventional chemotherapy resistance and probable hypothesis to develop it. It is known that tumor heterogeneity plays a fundamental essential role in cancer development and chemo resistance. Gastric Carcinoma Tumor initiating cell (GATIC) controls high tumerogenicity, maintenance of self renewal potential, formation of cancer and non cancer cells and chemotherapy resistance. Identifying the putative specific cell marker for purification and functional validation of GATIC, tracing the origin of GATIC, decoding the regulatory mechanism of GATIC, pave the way for the development of GATIC targeted therapy which is in phase of preclinical study and clinical trial. Alteration of tumor microenvironment is deeply implicated in tumor progression and metastasis in gastric cancer patient. Interaction between tumor cell and their microenvironment with cytokines and miRNA in extracellular vesicles such as exosome can have a substantial impact on tumor characteristics. Interaction and its clinical impact of alteration of GC microenvironment will be discussed. In the possible treatment hypothesis the level IL6, M1, CXCl12/CXCR may be blocked and the level of M2, C8+T cell and CCK2R may be amplified to develop TEM directed targeted therapy. After uncovering the mechanism of chemo resistance the differentiation therapy and elimination therapy of gastric carcinoma may be a sustainable targeted therapy. In this context over expression of ATOH1 in GATICS and Lentiviral vector based knockdown of PGK1 may be a treatment method to overcome Chemo resistance of GC. In the way of elimination therapy Cyclopamine and Vismodegib may be a feasible targeted therapy in GC. molecules which is specific suppressor of Wnt/B catenin may be used as a selective therapy for GATIC.
Citation Format: Kalyan Kusum Mukherjee, Dattatreya Mukherjee. Role of tumor heterogeneity, tumor microenvironment and tumor initiating cell in gastric carcinogenesis from the perspective of development of hypothesis for its clinical application [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-011.
Abstract PO-030: Characterizing mechanisms for inhibiting metastasis in triple negative breast cancer
Authors: Yang Dongbo , Dann Christopher , Pott Sebastian , Rosner Marsha 
Published: December 2020

Abstract
Tumor cell heterogeneity has been strongly implicated in metastatic progression of solid tumors such as breast cancer, leading to resistance and recurrence. We hypothesize that inhibiting metastasis will reduce tumor cell heterogeneity and thereby increase therapeutic sensitivity. To test this hypothesis, we expressed the metastasis suppressor Raf Kinase Inhibitory Protein (RKIP or PEBP1) in triple-negative breast cancer (TNBC) cells as a means of comparing the variation in gene expression between individual cells in metastatic versus non-metastatic tumors. Xenograft tumors with or without exogenous RKIP expression were dissociated into single cell suspensions. We removed mouse as well as dead cells, and the remaining cells were loaded onto a Fluidigm C1 high-throughput chip for separation and library preparation. For each condition we performed three independent experiments yielding a total of 1569 cells. We performed controls to ensure that differences were not due to batch effects, cell cycle stage or sample quality. Clustering of single cells across all samples indicated that gene expression profiles are similar, confirming reproducibility. Gene ontology analysis of differentially expressed genes between cells with and without RKIP overexpression reveals gene sets that are important in tumor cell transitions from metastatic to non-metastatic states. These data will allow us to specifically test whether metastatic tumors are more heterogeneous than non-metastatic tumors in TNBC.
Citation Format: Dongbo Yang, Christopher Dann, Sebastian Pott, Marsha Rosner. Characterizing mechanisms for inhibiting metastasis in triple negative breast cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-030.
Abstract PO-031: Innate immune genes distinguish the immune microenvironment of early onset colorectal cancer
Authors: Gardner Ivy H. , Siddarthan Ragavan , Watson Katherine , Dewey Elizabeth , Ruhl Rebecca , Guan Xiangnan , Xia Zheng , Tsikitis Liana V. , Anand Sudarshan 
Published: December 2020

Abstract
Despite a decrease in the incidence of colorectal cancer (CRC) over the last 40 years, the incidence of CRC in people under 50 years old is increasing around the globe. Early onset (≤50 years old) and late onset (≥65 years old) CRC appear to have differences in their clinicopathological and genetic features, but it is unclear if there are differences in the tumor microenvironment. We hypothesized that the immune microenvironment of early onset CRC is distinct from late onset CRC and promotes tumor progression. We used Nanostring immune profiling to analyze mRNA expression of immune genes in FFPE surgical specimens from patients with early (N=40) and late onset (N=39) CRC. We found three genes, SAA1, C7, and CFD, have increased expression in early onset colorectal cancer and distinct immune signatures based on the tumor location. After adjusting for clinicopathological features, increased expression of CFD and SAA1 were associated with worse progression free survival and increased expression of C7 was associated with worse overall survival. Our data demonstrate that the immune microenvironment in early onset CRC is unique, location dependent, and associated with worse outcomes. We propose that age specific immune signatures in the colorectal immune microenvironment can be used as biomarkers for prognosis as well as the development of targeted immune modulatory agents.
Citation Format: Ivy H. Gardner, Ragavan Siddarthan, Katherine Watson, Elizabeth Dewey, Rebecca Ruhl, Xiangnan Guan, Zheng Xia, Liana V. Tsikitis, Sudarshan Anand. Innate immune genes distinguish the immune microenvironment of early onset colorectal cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-031.
Abstract PO-057: Host cell-derived TXA2-mediated Gq signaling in tumor cells promotes tumor immune evasion
Authors: Terai Kenta , Konishi Yoshinobu , Ichise Hiroshi , Watabe Tetsuya , Sando Yukari , Kondo Takefumi , Oki Choji , Tsukiji Shinya , Hamazaki Yoko , Murakawa Yasuhiro , Takaori-Kondo Akifumi , Matsuda Michiyuki 
Published: December 2020

Abstract
Tumor-derived prostaglandin E2 (PGE2) promotes tumor progression through evasion of anti-tumor immunity. However, little is known about how PGE2 secretion is regulated within tumor tissues. Here, we show that host cell-derived thromboxane A2 (TXA2) triggers tumor cells to secrete PGE2, resulting in the evasion of anti-tumor immunity. An induction of Ca2+ transients in BrafV600E mouse melanoma cells is sufficient to trigger PGE2 secretion. The frequency of Ca2+ transients is markedly higher in melanoma cells implanted into mice than those in vitro. We show that t he melanoma cells deficient in TXA2 receptor or Gq subunit α do not exhibit Ca2+ transients in vivo nor evade anti-tumor immunity, as do not melanoma cells deficient in cyclooxygenases (COX). Motesanib, a VEGF receptor antagonist, suppresses Ca2+ transients, suggesting the involvement of tumor endothelial cells in the TXA2 production within tumor tissue. These resultsresults identifyresults identifyidentify TXA2 as a critical promotertargetof PGE2-dependent tumorigenesis.
Citation Format: Kenta Terai, Yoshinobu Konishi, Hiroshi Ichise, Tetsuya Watabe, Yukari Sando, Takefumi Kondo, Choji Oki, Shinya Tsukiji, Yoko Hamazaki, Yasuhiro Murakawa, Akifumi Takaori-Kondo, Michiyuki Matsuda. Host cell-derived TXA2-mediated Gq signaling in tumor cells promotes tumor immune evasion [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-057.