tbuckley/cabot-search huggingface dataset:
Abstract PO039: Novel <i>in vivo</i> imaging method to evaluate "Don't eat me" signal of tumor against microglia
Authors: Takahiro Tsuji, Hiroaki Wake, Mariko Shindo, Daisuke Kato, Hiroaki Ozasa, Toyohiro Hirai
Journal: Cancer Research (2021)

Abstract Tumor formation is promoted by increased expression of “Don’t eat me” signals such as CD47 in cancer cells that inhibit phagocytic action of macrophages. However, the signals can regulate generation of brain metastasis is still unclear. In the brain, microglia and perivascular macrophages are the only resident immune cells of the brain parenchyma. Here, we have developed an in-vivo imaging method that can allow us to evaluate microglial phagocytosis of tumor and to detemine the fates of cancer cells in the brain. The skull of the CX3CR1-EGFP mice, in which microglia is specifically labeled with EGFP, was replaced with a glass coverslip, and the fluorescently labeled lung cancer cells (CMT167-mCherry) were injected via the internal carotid artery of the mice. The fate of arrested cancer cells in the brain vascular was monitored for 12-16 days. Of the 324 cancer cells (4 mice), 49.8% (N=138) of cells displaced from their original site, 40.4% (N=112) of cells developed micro-metastasis, and 6.9% (N=27) of cells were processed by microglia resulting in cell death. To evaluate the “Don’t eat me” signal against microglia, a CD47 gene knockout cell line was monitored as well, and these cells developed significantly less micro-metastasizes compared with CD47 positive cells. This in vivo imaging of the brain metastasis potentially provide a method for monitoring of tumor fate and validation of crucial target. Citation Format: Takahiro Tsuji, Hiroaki Wake, Mariko Shindo, Daisuke Kato, Hiroaki Ozasa, Toyohiro Hirai. Novel in vivo imaging method to evaluate "Don't eat me" signal of tumor against microglia [abstract]. In: Proceedings of the AACR Virtual Special Conference on the Evolving Tumor Microenvironment in Cancer Progression: Mechanisms and Emerging Therapeutic Opportunities; in association with the Tumor Microenvironment (TME) Working Group; 2021 Jan 11-12. Philadelphia (PA): AACR; Cancer Res 2021;81(5 Suppl):Abstract nr PO039.
OP0112 Nonspine fractures are associated with physical impairment
Authors: PD Ross, JW Davis, J Chandler, RD Wasnich
Journal: Annals of the Rheumatic Diseases (2001)

<h3>Background</h3> There have been few studies of physical impairment following nonspine fractures. <h3>Objectives</h3> To examine this issue among 705 Japanese women in Hawaii. <h3>Methods</h3> Only new fractures that had occurred during 13 years of follow up were considered; 121 women had 1, and 26 women had 2 or more new nonviolent, nonspine fractures. Activities of daily living (ADLs) and measures of physical performance (PP) were measured at the end of follow up. Associations with new nonspine fractures were evaluated using logistic regression analysis adjusted for age, height, body mass index, prior vertebral fractures, and prior nonspine fractures. <h3>Results</h3> Women with new fractures had significantly greater difficulty with 10 out of 13 ADLs, with odds ratios of 1.6 to 2.9. The associations tended to be stronger for fractures within the prior 5 years; only 2 ADLs were significantly associated with fractures that had occurred more than 5 years earlier. For most ADLs, associations with hip, rib, and upper arm fractures were generally stronger (odd ratios &gt;2.3) than for wrist, foot, or lower leg fractures (odds ratios &lt; 2.0). Overall, nonspine fractures were significantly associated with 25% slower walking speed and longer time to complete the chair stand test, but not &nbsp;with other PP measures. However, hip fractures were associated with lower performance on 5 out of 6 PPs. <h3>Conclusion</h3> We conclude that nonspine fractures may be associated with increased physical impairment for up to 5 years later, and that the severity appears to vary by fracture location.
Abstract 3806: Cigarette smoke extract permits survival of <i>TET2-/-</i> and <i>JAK2V617F</i> hematopoietic cells
Authors: Gajalakshmi Ramanathan, Brianna Craver, Rebecca J. Arechavala, David Herman, Michael T. Kleinman, Angela G. Fleischman
Journal: Cancer Research (2020)

Abstract Inactivating somatic mutations in the ten-eleven translocation 2 (TET2) gene is commonly found in clonal hematopoiesis (CH) and contributes to the pathogenesis of myeloid malignancies such as myeloproliferative neoplasms (MPN), myelodysplastic syndrome and acute myeloid leukemia. Incidentally, smoking behavior is associated with CH and we hypothesize that TET2 mutant hematopoietic cells are resistant to the deleterious effects of smoke exposure. Cigarette smoke extract (CSE) was prepared from mainstream cigarette smoke using a standard protocol and volume/volume percentage (v/v %) dilutions used for in vitro exposures. Lineage negative bone marrow cells isolated from TET2 wildtype (TET2+/+) and TET2 knockout (TET-/-) mice were exposed to CSE and cultured in methylcellulose containing semi-solid medium to assess myeloid colony formation. Cells were also grown in liquid culture under long-term culture conditions to demonstrate the effect of CSE on cell proliferation. Peripheral blood mononuclear cells from JAK2V617F positive MPN patients were treated with CSE for colony forming assays. TET2+/+ bone marrow cells showed decreased myeloid colony formation in the presence of CSE while TET2-/- cells were not significantly affected by CSE. Similarly in liquid cultures, TET2-/- lineage negative cells expanded significantly compared to their wildtype counterparts indicating resistance to the growth suppressive effects of CSE. The JAK2V617F mutation is the most common somatic mutation found in MPN patients and we observed that the suppressive effect of CSE on myeloid colony formation was more pronounced in normal subjects than JAK2V617F positive MPN subjects. This suggests that CH associated somatic mutations such as in TET2 promote resistance of bone marrow progenitors to environmental stressors like cigarette smoke, possibly via anti-apoptotic mechanisms. Future studies include studying the effects of inhalation exposure of combustible and electronic cigarette smoke on TET2-/- and JAK2V617F hematopoiesis in competitive bone marrow transplanted mice. Citation Format: Gajalakshmi Ramanathan, Brianna Craver, Rebecca J. Arechavala, David Herman, Michael T. Kleinman, Angela G. Fleischman. Cigarette smoke extract permits survival of TET2-/- and JAK2V617F hematopoietic cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3806.
Abstract 347: Neogenin as an anti-invasive target for diffuse intrinsic pontine gliomas
Authors: Julie Sesen, Jessica Driscoll, Edward Smith
Journal: Cancer Research (2020)

Abstract Introduction. Diffuse Intrinsic Pontine Glioma (DIPG) is a rare high-grade tumor of the brainstem that occurs almost exclusively in children. The significant mortality rates of DIPG stem largely from its capacity to invade adjacent normal brain. We have previously published studies identifying the axon guidance factor netrin-1 and its receptor neogenin as key drivers regulating brain tumor invasion in medulloblastoma and glioblastoma. Here we expand this work to investigate the role of netrin-1 and neogenin in DIPG and identify them as putative biomarkers and governors of tumor invasion. Methods. Urine of 49 DIPG patients and 42 age- and sex-matched controls was collected. Netrin-1 expression was quantified by ELISA. Results were subjected to univariate and multivariate statistical analyses and compared between clinical cohorts. In vitro experiments with established DIPG cell lines utilized RTqPCR, Western blot and flow cytometry to quantify expression of netrin-1 and neogenin. The effect of neogenin blockade on viability and invasion was assessed by flow cytometry (n=3) and transwell chamber assays (n=3) respectively. Results. Patient samples revealed a significantly low level of urinary netrin-1 compared to matched controls (p&amp;lt;0.005). This result was corroborated with cell lines in vitro. Interestingly, its receptor neogenin was upregulated in these cells when compared to control glial cells when quantified by mRNA, protein and FACS analysis. Blockade of neogenin in DIPG cell lines resulted in an increase of cell death and a significant decrease of cell invasion. Conclusion. Expanding on previous work, this data suggests that urinary levels of netrin-1 may have utility as a non-invasive biomarker for DIPG. Our data demonstrates the vital role of neogenin as a regulator of tumor invasion and survival in DIPG. The blockade of neogenin in DIPG cells also demonstrates the potential utility of neogenin as a cell-surface druggable target, capable of reducing tumor invasion and increasing tumor cell death. Citation Format: Julie Sesen, Jessica Driscoll, Edward Smith. Neogenin as an anti-invasive target for diffuse intrinsic pontine gliomas [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 347.
Abstract 3977: Stromal BMP signaling imbalance mediated by GREM1 and ISLR regulates colorectal cancer progression
Authors: Hiroki Kobayashi, Krystyna A. Gieniec, Tongtong Wang, Josephine A. Wright, Nobumi Suzuki, Tamsin RM Lannagan, Yoku Hayakawa, Simon J. Leedham, Nicholas Arpaia, Siddhartha Mukherjee, Timothy C. Wang, Atsushi Enomoto, Masahide Takahashi, Daniel L. Worthley, Susan L. Woods
Journal: Cancer Research (2020)

Abstract Introduction Cancer-associated fibroblasts (CAFs), a heterogeneous component of the tumor microenvironment, substantially influence tumor progression. Bone morphogenetic proteins (BMP) play a critical part in defining the intestinal epithelial niche and either promote or retard cancer progression in a context-dependent manner. However, the role of BMP signaling in the colorectal cancer (CRC) stroma remains to be fully elucidated. This study investigated the significance of mesenchymal BMP signaling as a potential therapeutic target in CRC progression. Design Using CRC expression array data, we identified two CAF-specific factors involved in BMP signaling, then verified their upregulation in the human CRC stroma by in-situ hybridization (ISH). We took advantage of a preclinical mouse model of CRC hepatic metastasis to test approaches targeting the BMP signaling pathway. Results CRC microarray data identified GREM1 and ISLR as CAF-specific genes involved in BMP signaling. In colonic myofibroblasts, Grem1-overexpression inhibited BMP signaling whereas BMP7 signaling was augmented by Islr overexpression, suggesting opposing roles for GREM1 and ISLR in the regulation of BMP signaling. ISH using human rectal cancer samples revealed that GREM1 and ISLR were expressed in distinct CAF subpopulations and that GREM1 and ISLR expression predicted poor and favorable survival, respectively. Notably, Grem1 and Islr expression was differentially regulated by Foxl1, an intestinal mesenchyme-lineage transcription factor, and TGF-b, indicating a mechanism for generating fibroblast heterogeneity. Finally, adeno-associated virus 8-mediated in-vivo overexpression of Islr in hepatocytes retarded growth and generated more differentiated histology in CRC hepatic metastases. Conclusion These data suggest that increased stromal BMP signaling may ameliorate CRC progression and provide a rationale for targeting stromal BMP signaling to inhibit CRC progression and metastasis. Citation Format: Hiroki Kobayashi, Krystyna A. Gieniec, Tongtong Wang, Josephine A. Wright, Nobumi Suzuki, Tamsin RM Lannagan, Yoku Hayakawa, Simon J. Leedham, Nicholas Arpaia, Siddhartha Mukherjee, Timothy C. Wang, Atsushi Enomoto, Masahide Takahashi, Daniel L. Worthley, Susan L. Woods. Stromal BMP signaling imbalance mediated by GREM1 and ISLR regulates colorectal cancer progression [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3977.
The PD-1 expression balance between effector and regulatory T cells predicts the clinical efficacy of PD-1 blockade therapies
Authors: Shogo Kumagai, Yosuke Togashi, Takahiro Kamada, Eri Sugiyama, Hitomi Nishinakamura, Yoshiko Takeuchi, Kochin Vitaly, Kota Itahashi, Yuka Maeda, Shigeyuki Matsui, Takuma Shibahara, Yasuho Yamashita, Takuma Irie, Ayaka Tsuge, Shota Fukuoka, Akihito Kawazoe, Hibiki Udagawa, Keisuke Kirita, Keiju Aokage, Genichiro Ishii, Takeshi Kuwata, Kenta Nakama, Masahito Kawazu, Toshihide Ueno, Naoya Yamazaki, Koichi Goto, Masahiro Tsuboi, Hiroyuki Mano, Toshihiko Doi, Kohei Shitara, Hiroyoshi Nishikawa
Journal: Nature Immunology (2020)
Systems genetics analysis identifies calcium-signaling defects as novel cause of congenital heart disease
Authors: Jose M. G. Izarzugaza, Sabrina G. Ellesøe, Canan Doganli, Natasja Spring Ehlers, Marlene D. Dalgaard, Enrique Audain, Gregor Dombrowsky, Karina Banasik, Alejandro Sifrim, Anna Wilsdon, Bernard Thienpont, Jeroen Breckpot, Marc Gewillig, Hashim Abdul-Khaliq, Hans-Heiner Kramer, Felix Berger, Brigitte Stiller, Ulrike Bauer, Thomas Pickardt, Sabine Klaassen, J. David Brook, Marc-Phillip Hitz, Lars A. Larsen, Søren Brunak
Journal: Genome Medicine (2020)

Abstract Background Congenital heart disease (CHD) occurs in almost 1% of newborn children and is considered a multifactorial disorder. CHD may segregate in families due to significant contribution of genetic factors in the disease etiology. The aim of the study was to identify pathophysiological mechanisms in families segregating CHD. Methods We used whole exome sequencing to identify rare genetic variants in ninety consenting participants from 32 Danish families with recurrent CHD. We applied a systems biology approach to identify developmental mechanisms influenced by accumulation of rare variants. We used an independent cohort of 714 CHD cases and 4922 controls for replication and performed functional investigations using zebrafish as in vivo model. Results We identified 1785 genes, in which rare alleles were shared between affected individuals within a family. These genes were enriched for known cardiac developmental genes, and 218 of these genes were mutated in more than one family. Our analysis revealed a functional cluster, enriched for proteins with a known participation in calcium signaling. Replication in an independent cohort confirmed increased mutation burden of calcium-signaling genes in CHD patients. Functional investigation of zebrafish orthologues of ITPR1 , PLCB2 , and ADCY2 verified a role in cardiac development and suggests a combinatorial effect of inactivation of these genes. Conclusions The study identifies abnormal calcium signaling as a novel pathophysiological mechanism in human CHD and confirms the complex genetic architecture underlying CHD.
Ultra-Long-term Follow-up of Interferon Alfa Treatment for HBeAg-Positive Chronic Hepatitis B Virus Infection
Authors: Hannah S.J. Choi, Margo J.H. van Campenhout, Anneke J. van Vuuren, Lisette A.P. Krassenburg, Milan J. Sonneveld, Robert J. de Knegt, Bettina E. Hansen, Harry L.A. Janssen
Journal: Clinical Gastroenterology and Hepatology (2020)
Abstract 4276: Target enrichment to enable RNA-sequencing on FFPE samples: Application to a patient selection biomarkers in colorectal cancer
Authors: Maximilian Rogers-Grazado, Joachim Theilhaber, Jack Pollard, Alexei Protopopov
Journal: Cancer Research (2020)

Abstract In proof of concept clinical studies, selecting for patients that are the most likely to respond to a given therapy will increase the chance of demonstrating clinical benefit for a new investigational agent. Archived Formalin-Fixed, Paraffin-Embedded (FFPE) tissue taken at the time of first biopsy and cancer diagnosis are a ready source of material for such patient selection assays; however if the selection assay is RNA-based sequencing based assay, FFPE tumor tissues are typically refractory to standard methods. Here we describe Target Enrichment, an RNA-sequencing technique that enabled analysis of FFPE tumor tissue. The Target Enrichment technique provides the necessary, high quality gene expression data required for identifying the mesenchymal subtype of CRC. In this experiment, RNA was extracted from a set of 192 histologically characterized, archived colorectal cancer (CRC) FFPE tumor tissues with sufficient representation of all Consensus Molecular Subtypes of CRC. A major issue with FFPE tissue is that nucleic acids are not well preserved in the fixation process. The RNA extraction method was carefully optimized in advance toward improving yield and integrity of the total RNA. In order to accommodate the low FFPE RNA integrity, we used Target Enrichment, a technique derived from whole-exome sequencing that isolates and amplifies library fragments corresponding to only the transcribed regions of interest. After testing several protocols, we established a Target Enrichment technique to remove low-quality library fragments that would otherwise interfere and impair sequencing quality. This method allowed us to generate high-quality sequencing data for samples that proved challenging using traditional RNA-seq methods. Fresh-frozen tissue samples were used as a benchmark and our Target Enrichment technique showed comparable performance across multiple sequencing quality metrics including mapping rate, expression profiling efficiency, number of genes detected, also the pass rate. Furthermore, data generated using our Target Enrichment technique aligned with the known frequencies of the Consensus Molecular Subtypes of CRC. Overall, our Target Enrichment technique provides a protocol for generating high quality RNA-seq libraries from highly degraded FFPE RNA. Citation Format: Maximilian Rogers-Grazado, Joachim Theilhaber, Jack Pollard, Alexei Protopopov. Target enrichment to enable RNA-sequencing on FFPE samples: Application to a patient selection biomarkers in colorectal cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4276.
Abstract 1980: Multiplex digital PCR combined with melting curve analysis for detecting <i>KRAS</i> and <i>BRAF</i> mutations
Authors: Junko Tanaka, Tatsuo Nakagawa, Akiko Shiratori, Kunio Harada, Chihiro Uematsu, Erina Takai, Shinichi Yachida
Journal: Cancer Research (2020)

Abstract Background Digital PCR (dPCR) is a promising method for liquid biopsies and is able to quantify nucleic acids more sensitively than real-time PCR. However, dPCR has a large fluctuation in the fluorescence intensity of the droplets or wells due to insufficient PCR in the small partitions, limiting the multiplexing capability of using the fluorescence intensity. In this study, we propose a new measurement method that combines dPCR with melting curve analysis for highly multiplexed genotyping. Methods A sample is digitized into a silicon chip with up to ~104 wells in which asymmetric PCR was performed to obtain more single-stranded amplicons that are complimentary to molecular beacon probes. Fluorescence images were captured while controlling the temperature of the chip, and melting curve was measured for each well. Then, genotyping was performed by using the fluorescence intensity, dye color of the probe, and melting temperature (Tm). Because the Tm of the PCR products does not considerably depend on the amplification efficiency of PCR, genotyping accuracy is improved by using Tm values, enabling highly multiplexed genotyping. Results The concept was confirmed by measuring four common KRAS mutations (G12D, G12V, G12R, and G13D) and one common BRAF mutation (V600E). G12D, G12V and G12R-mutant KRAS alleles were detected with FAM-labeled probes, G13D-mutant KRAS allele and wildtype KRAS allele were detected with HEX-labeled probes, and V600E-mutant BRAF allele and wildtype BRAF allele were detected with CAL Fluor Red 610-labeled probes. The results showed that the peaks of the Tm distributions of the DNA groups were separated by more than 2°C. By combining the fluorescence intensities and the Tm values, the wildtype and mutant groups were clearly identified and able to be quantified. Conclusion We have proposed a new measurement method that combines dPCR with melting curve analysis, and successfully performed the multiplexed genotyping assay. To our knowledge, this is the first demonstration of genotyping of seven DNA groups with a single mutation of cancer-related genes by combining dPCR with melting curve analysis. Citation Format: Junko Tanaka, Tatsuo Nakagawa, Akiko Shiratori, Kunio Harada, Chihiro Uematsu, Erina Takai, Shinichi Yachida. Multiplex digital PCR combined with melting curve analysis for detecting KRAS and BRAF mutations [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1980.