tbuckley/cabot-search huggingface dataset:
Single-Cell Analysis of the Multicellular Ecosystem in Viral Carcinogenesis by HTLV-1
Authors: Junji Koya, Yuki Saito, Takuro Kameda, Yasunori Kogure, Mitsuhiro Yuasa, Joji Nagasaki, Marni B. McClure, Sumito Shingaki, Mariko Tabata, Yuki Tahira, Keiichi Akizuki, Ayako Kamiunten, Masaaki Sekine, Kotaro Shide, Yoko Kubuki, Tomonori Hidaka, Akira Kitanaka, Nobuaki Nakano, Atae Utsunomiya, Yosuke Togashi, Seishi Ogawa, Kazuya Shimoda, Keisuke Kataoka
Journal: Blood Cancer Discovery (2021)

Abstract Premalignant clonal expansion of human T-cell leukemia virus type-1 (HTLV-1)–infected cells occurs before viral carcinogenesis. Here we characterize premalignant cells and the multicellular ecosystem in HTLV-1 infection with and without adult T-cell leukemia/lymphoma (ATL) by genome sequencing and single-cell simultaneous transcriptome and T/B-cell receptor sequencing with surface protein analysis. We distinguish malignant phenotypes caused by HTLV-1 infection and leukemogenesis and dissect clonal evolution of malignant cells with different clinical behavior. Within HTLV-1–infected cells, a regulatory T-cell phenotype associates with premalignant clonal expansion. We also delineate differences between virus- and tumor-related changes in the nonmalignant hematopoietic pool, including tumor-specific myeloid propagation. In a newly generated conditional knockout mouse model recapitulating T-cell–restricted CD274 (encoding PD-L1) gene lesions found in ATL, we demonstrate that PD-L1 overexpressed by T cells is transferred to surrounding cells, leading to their PD-L1 upregulation. Our findings provide insights into clonal evolution and immune landscape of multistep virus carcinogenesis. Significance: Our multimodal single-cell analyses comprehensively dissect the cellular and molecular alterations of the peripheral blood in HTLV-1 infection, with and without progression to leukemia. This study not only sheds light on premalignant clonal expansion in viral carcinogenesis, but also helps to devise novel diagnostic and therapeutic strategies for HTLV-1–related disorders. This article is highlighted in the In This Issue feature, p. 403
Abstract 1443: CHKing melanoma: CHK1 inhibitor +low dose hydroxyurea triggers immunogenic cell death and immunostimulatory cytokine expression to drive an anti-tumor immune response
Authors: Brian G. Gabrielli, Martina Proctor, Jazmina Gonzalez Cruz, Bijun Zeng, Riccardo Dolcetti, Colm Keane, Nikolas Haass, James Wells
Journal: Cancer Research (2021)

Abstract About half of melanomas respond to immunotherapy, but we currently lack reliable markers to identify likely responders. Therefore, a large number of patients receive this expensive therapy for no benefit. We have previously shown that inhibition of the cell cycle regulator, Checkpoint kinase 1 (CHK1), with subclinical dose of the replication stress inducer hydroxyurea is cytotoxic in a high proportion of melanomas tested. We now report that CHK1 inhibitor + low dose hydroxyurea (LDHU) treatment triggers immunostimulatory cytokine and chemokine expression, and an immunogenic form of cell death. In xenograft models, the drug combination blocks tumor growth for extended periods after the completion of treatment. In syngeneic mouse melanoma models, the drug combination also effectively controls tumor growth and induces regression in a proportion of cases. It also increases immune cell infiltration and activation of a tumor directed cytotoxic T cell response. We also demonstrate that the drug combination does not adversely affect an adaptive immune response or rapidly proliferating human T cells. The mechanism by which drug treatment promotes cytokine expression is unlikely to involve the cGAS-STING signalling pathway which is commonly defective in melanomas. Using two engineered mouse melanoma models we have found that CHK1 inhibitor + LDHU increases cytotoxic CD8+ T cells and NK cell infiltration and activation, but we have also found increased CD4+ Treg tumor infiltration and increased CD8+ T cell PD-1 expression. We have also found increased expression of other immune checkpoint regulators. This indicates a strong anti-tumor immune response is initiated but immune suppression and T cell exhaustion have limited the extent of the response of the tumor infiltrating T cells. However, circulating T cells retained strong anti-tumor activity. The harvested tumors from the drug combination treated mice that do increase in size after treatment show strong evidence of cytotoxic activity. These data provide evidence that CHK1 inhibitors + LDHU is well tolerated and triggers a strong anti-cancer immune response that should combine with immune therapy, although the selection of the target of the immunotherapy will be critical for successfully overcoming the immune suppression triggered. Citation Format: Brian G. Gabrielli, Martina Proctor, Jazmina Gonzalez Cruz, Bijun Zeng, Riccardo Dolcetti, Colm Keane, Nikolas Haass, James Wells. CHKing melanoma: CHK1 inhibitor +low dose hydroxyurea triggers immunogenic cell death and immunostimulatory cytokine expression to drive an anti-tumor immune response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1443.
Is it safe to replace ReTUR in high grade T1 non-muscle invasive bladder cancer patients with urine cytology and in-office cystoscopy? Preliminary results from an ongoing prospective multicenter trial
Authors: R. Contieri, R. Hurle, A. Saita, P. Casale, G. Lughezzani, M. Lazzeri, G. Taverna, F. Greco, S. Barra, G. Muto, M. Paciotti, P.P. Avolio, N. Frego, P. Diana, A. Uleri, D. Maffei, V. Fasulo, L. Domanico, N.M. Buffi, G. Guazzoni
Journal: European Urology (2021)
Performance of the Innova SARS-CoV-2 antigen rapid lateral flow test in the Liverpool asymptomatic testing pilot: population based cohort study
Authors: Marta García-Fiñana, David M Hughes, Christopher P Cheyne, Girvan Burnside, Mark Stockbridge, Tom A Fowler, Veronica L Fowler, Mark H Wilcox, Malcolm G Semple, Iain Buchan
Journal: BMJ (2021)

Abstract Objective To assess the performance of the SARS-CoV-2 antigen rapid lateral flow test (LFT) versus polymerase chain reaction testing in the asymptomatic general population attending testing centres. Design Observational cohort study. Setting Community LFT pilot at covid-19 testing sites in Liverpool, UK. Participants 5869 asymptomatic adults (≥18 years) voluntarily attending one of 48 testing sites during 6-29 November 2020. Interventions Participants were tested using both an Innova LFT and a quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) test based on supervised self-administered swabbing at testing sites. Main outcome measures Sensitivity, specificity, and predictive values of LFT compared with RT-qPCR in an epidemic steady state of covid-19 among adults with no classic symptoms of the disease. Results Of 5869 test results, 22 (0.4%) LFT results and 343 (5.8%) RT-qPCR results were void (that is, when the control line fails to appear within 30 minutes). Excluding the void results, the LFT versus RT-qPCR showed a sensitivity of 40.0% (95% confidence interval 28.5% to 52.4%; 28/70), specificity of 99.9% (99.8% to 99.99%; 5431/5434), positive predictive value of 90.3% (74.2% to 98.0%; 28/31), and negative predictive value of 99.2% (99.0% to 99.4%; 5431/5473). When the void samples were assumed to be negative, a sensitivity was observed for LFT of 37.8% (26.8% to 49.9%; 28/74), specificity of 99.6% (99.4% to 99.8%; 5431/5452), positive predictive value of 84.8% (68.1% to 94.9%; 28/33), and negative predictive value of 93.4% (92.7% to 94.0%; 5431/5814). The sensitivity in participants with an RT-qPCR cycle threshold (Ct) of &lt;18.3 (approximate viral loads &gt;10 6 RNA copies/mL) was 90.9% (58.7% to 99.8%; 10/11), a Ct of &lt;24.4 (&gt;10 4 RNA copies/mL) was 69.4% (51.9% to 83.7%; 25/36), and a Ct of &gt;24.4 (&lt;10 4 RNA copies/mL) was 9.7% (1.9% to 23.7%; 3/34). LFT is likely to detect at least three fifths and at most 998 in every 1000 people with a positive RT-qPCR test result with high viral load. Conclusions The Innova LFT can be useful for identifying infections among adults who report no symptoms of covid-19, particularly those with high viral load who are more likely to infect others. The number of asymptomatic adults with lower Ct (indicating higher viral load) missed by LFT, although small, should be considered when using single LFT in high consequence settings. Clear and accurate communication with the public about how to interpret test results is important, given the chance of missing some cases, even at high viral loads. Further research is needed to understand how infectiousness is reflected in the viral antigen shedding detected by LFT versus the viral loads approximated by RT-qPCR.
Abstract 121: A genetic signature of cancer dormancy: implications for human disease derived from a novel murine model
Authors: Anthony S. Casabianca, Crissy Dudgeon, Chris Harris, Subhajyoto De, Mihir Shah, Arthur Roberts, Eric Collisson, Vinod Balachandran, Darren Carpizo
Journal: Cancer Research (2021)

Abstract Pancreatic cancer (PC) is a highly lethal malignancy characterized by local tumor aggressiveness and early metastatic dissemination. While surgical resection is used to treat localized cancers, the majority of patients do recur suggesting the presence of disseminated tumor cells (DTC) at the time of surgery. These DTC's represent minimal residual disease. While most patients recur early, a subset recur late due to the reactivation of dormant tumor cells. Currently, the mechanisms of cancer dormancy are poorly understood in part due to a lack of animal models that reflect human disease. Here we describe a murine model of PC dormancy that mimics outcomes in resected human patients. Using single-cell transcriptomics and an assay for chromatin accessibility, we found dormancy is a distinct cellular state from pre or post-dormant cancer cells. Mechanisms of dormancy include increased expression of transcriptional repressor Dec2, which functionally drives quiescence, and monoallelic suppression of mutant KRAS by DNA methylation. Pathway analysis of dormant tumor cell transcriptomics indicated an up-regulation of enzymes involved in linoleic acid metabolism among others. Linoleic acid treatment of tumor cells resulted in inhibited cell proliferation, decreased tumor growth, and an increase in Dec2 expression. We have identified a dormancy gene signature that is distinct from non-dormant PC cells and found that this correlates with human resected patients with long term survivals, and inversely in patients with short term survivals. We demonstrate that dormancy is characterized by large scale transcriptomic changes and global chromatin remodeling. We developed methods for isolating DTCs from the livers of early stage PC patients undergoing resection. Using these methods we have found that the murine dormancy signature correlated with the gene expression of the DTCs and not primary tumor cells indicating this dormancy signature has human relevance with potential novel therapeutic avenues. Citation Format: Anthony S. Casabianca, Crissy Dudgeon, Chris Harris, Subhajyoto De, Mihir Shah, Arthur Roberts, Eric Collisson, Vinod Balachandran, Darren Carpizo. A genetic signature of cancer dormancy: implications for human disease derived from a novel murine model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 121.
Abstract 3081: Secretory human ribonuclease 1 functions as Eph receptor A4 ligand to promote breast tumor initiation
Authors: Ying-Nai Wang, Heng-Huan Lee, Wen-Hao Yang, Gabriel N. Hortobagyi, Dihua Yu, Mien-Chie Hung
Journal: Cancer Research (2021)

Abstract The pancreatic human ribonuclease (hRNase) A superfamily is comprised of eight canonical hRNases, including hRNase 1, all of which can be detected in various body fluids, e.g., serum and plasma. Secretory hRNase 1 exerts its ribonucleolytic activity to function in extracellular RNA clearance. Moreover, hRNase 1 regulates hemostasis, inflammation, and innate immunity, indicating that hRNase 1 possesses multiple functions in addition to RNA clearance. Studies on hRNase 1 have been extensively investigated the biochemical properties and post-translational modifications, such as glycosylation. Nonetheless, the biological function of hRNase1 and whether it plays a role in cancer have not yet been completely defined. Recent studies indicated that hRNase 5 serves as a ligand for the receptor tyrosine kinase (RTK) epidermal growth factor receptor and plexin-B2 receptor in solid and hematopoietic cancers. Those findings reveal a role of the hRNase A superfamily in tumor progression and an unconventional ligand-receptor relationship between RNase and RTK families. Here, we demonstrate that hRNase 1, independently its ribonucleolytic activity, enriches the stem-like cell population and enhances the tumor-initiating ability of breast cancer cells. Specifically, secretory hRNase 1 binds to and activates the RTK Eph receptor A4 (EphA4) signaling to promote breast tumor initiation in an autocrine/paracrine manner, which is distinct from the classical ligand-receptor ephrin-EphA4 juxtacrine signaling through contact-dependent cell-cell communication. In addition, analysis of human breast tumor tissue microarrays reveals a positive correlation between hRNase 1, EphA4 activation, and stem cell marker CD133. Notably, high hRNase 1 level in plasma samples is positively associated with EphA4 activation in tumor tissues from the paired breast cancer patients, highlighting the pathological relevance of the hRNase 1-EphA4 axis in breast cancer. The discovery of hRNase 1 as a secretory ligand of EphA4 to enhance breast cancer stemness suggests a potential treatment strategy for breast cancer by inactivating the hRNase 1-EphA4 axis. Citation Format: Ying-Nai Wang, Heng-Huan Lee, Wen-Hao Yang, Gabriel N. Hortobagyi, Dihua Yu, Mien-Chie Hung. Secretory human ribonuclease 1 functions as Eph receptor A4 ligand to promote breast tumor initiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3081.
TISU (Therepeutic Intervention for Stones in the Ureter): ESWL versus Ureteroscopy, a multicentre RCT
Authors: R. Dasgupta, S. Cameron, L. Aucott, G. Maclennan, R.E. Thomas, J. N’dow, J. Norrie, K. Anson, F.X. Keeley, S. Maclennan, K. Starr, S. Mcclinton
Journal: European Urology (2021)
Abstract LB201: Understanding genetic variation in cancer using nanopore targeted sequencing
Authors: Shruti V. Iyer, Melissa Kramer, Sara Goodwin, W. Richard McCombie
Journal: Cancer Research (2021)

Abstract Structural variations (SV), a hallmark of genomic instability in cancer can either activate oncogenes or inactivate tumor suppressor genes. SVs tend to be recurrent and have been associated with several cancer types. Next-generation sequencing (NGS) is mostly blind to large SVs, lacking sensitivity with false positive rates up to 89% in SV detection. Long-read, single-molecule sequencing platforms can address larger variations as they typically generate read lengths of tens of thousands of bases and have helped identify thousands of genomic features pertinent to cancer that were previously missed by short-read sequencing. However, the throughput and coverage offered by whole genome long read sequencing makes it infeasible to conduct large-scale genomic studies.Targeted sequencing significantly improves accuracy and coverage by offering the depth necessary to detect rare alleles in a heterogenous population of cells. Using the nanopore Cas9-targeted sequencing (nCATS), a PCR-free enrichment system from Oxford Nanopore Technologies, we targeted 10 prominent cancer genes in MCF 10A and SK-BR-3 breast cell lines. However, we observed that the number of reads generated for targets longer than 30kb were not sufficient to accurately call SVs. To further enhance this approach, we developed an Affinity-based Cas-9-Mediated Enrichment (ACME) step, that uses HisTag DynabeadsTM to pulldown non-target reads. With ACME we achieved ~ 75-fold enrichment of the BRCA2 region and 35-65x coverage of this ~90 kb target on our panel. We observed an increase in enrichment and coverage of other genes on the panel as well, with enrichment as high as 5000-fold for some genes. While ACME is a biochemical approach, recently, adaptive sequencing or “Read Until”, a computational approach that ‘rejects' non-target reads has been used by a couple of groups for target enrichment. Using UNCALLED, a variation of Read Until, we observed an ~10x coverage of our targets. Recognizing the potential and limitations of both, biochemical and computational approaches, our efforts now are directed towards a combined approach where we expect to achieve a minimum enrichment of 200-fold across all targets. With a 200-fold enrichment of a 3.5Mb target, we should get between 200x - 400x coverage of the target, which should be high enough to detect SVs in as low as 10% of the cells in the sample. This would support large scale SV analysis to help define the landscape of such variants in the population and identify regions of therapeutic or diagnostic interest. Citation Format: Shruti V. Iyer, Melissa Kramer, Sara Goodwin, W. Richard McCombie. Understanding genetic variation in cancer using nanopore targeted sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB201.
Abstract 1423: Shikonin impairs the growth of docetaxel-resistant prostate cancer cells by necroptosis
Authors: Sascha D. Markowitsch, Kira M. Juetter, Patricia Schupp, Kristine Hausschulte, Olesya Vakhrusheva, Jindrich Cinatl, Martin Michaelis, Thomas Efferth, Axel Haferkamp, Eva Juengel
Journal: Cancer Research (2021)

Abstract Introduction: Prostate carcinoma (PCa) is the most common malignancy in men. Androgen-targeted therapy and chemotherapy are currently the treatment of choice for advanced stages. Due to resistance towards these therapies, prognosis remains poor and new treatment options are urgently required. Shikonin (SHI) from Traditional Chinese Medicine (TCM) might be promising, since it induces anti-tumor effects in different tumor entities. However, data on PCa are few, and data on resistant PCa are not existent. Material and Methods: Parental (=sensitive) and docetaxel-resistant PCa cell lines, PC3, DU145, LNCaP, and 22Rv1 were exposed to SHI [0.1 - 1.5 μM] for 24, 48, or 72 hours. Untreated cells served as controls. Tumor cell growth, proliferation, cell cycle, and the expression of cell cycle regulating proteins were assessed. Several cell deaths, like apoptosis, necrosis and necroptosis as well as the metabolic activity were evaluated. Results: Time- and dose-dependent exposure to SHI significantly reduced tumor cell growth and proliferation in parental and docetaxel-resistant PCa cells, compared to the untreated controls. This was accompanied by cell cycle arrest in the G2/M phase in parental PC3 and docetaxel-resistant DU145 and S phase arrest in resistant 22Rv1, associated with modulated expression of cell cycle regulating proteins. Significant apoptotic effects were observed in parental and docetaxel-resistant PC3, DU145, 22Rv1, and resistant LNCaP. Moreover, SHI induced necroptosis in all parental and resistant PCa cells, as shown by additional application to the necroptosis inhibitor necrostatin-1. In line with this, RIP-1 expression enhanced under SHI exposure. In contrast, SHI did not alter the metabolic activity of the PCa cells. Conclusion: Significant anti-tumor effects are apparent in parental but also in docetaxel-resistant PCa cells after SHI application. Thus, adding SHI to standard therapies might be a promising treatment strategy for patients with advanced prostate cancer. Further investigations are necessary to verify our findings. Funding: Friedrich-Spicker-Stiftung (2017). Acknowledgments: The main portion of the results presented here are part of the MD thesis of Kira M. Juetter at the Department of Urology and Pediatric Urology, University Medical Center Mainz, Langenbeckstraße 1, 55131 Mainz, Germany. Citation Format: Sascha D. Markowitsch, Kira M. Juetter, Patricia Schupp, Kristine Hausschulte, Olesya Vakhrusheva, Jindrich Cinatl, Martin Michaelis, Thomas Efferth, Axel Haferkamp, Eva Juengel. Shikonin impairs the growth of docetaxel-resistant prostate cancer cells by necroptosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1423.
Azithromycin versus standard care in patients with mild-to-moderate COVID-19 (ATOMIC2): an open-label, randomised trial
Authors: Timothy S C Hinks, Lucy Cureton, Ruth Knight, Ariel Wang, Jennifer L Cane, Vicki S Barber, Joanna Black, Susan J Dutton, James Melhorn, Maisha Jabeen, Phil Moss, Rajendar Garlapati, Tanya Baron, Graham Johnson, Fleur Cantle, David Clarke, Samer Elkhodair, Jonathan Underwood, Daniel Lasserson, Ian D Pavord, Sophie Morgan, Duncan Richards
Journal: The Lancet Respiratory Medicine (2021)
Efficacy of fesoterodine fumarate in Neurogenic Detrusor Overactivity (NDO) due to Spinal Cord Lesion (SCL) or Multiple Sclerosis (MS) – A prospective study
Authors: C. Konstantinidis, M. Samarinas, M. Tzitzika, C. Thomas, Z. Kratiras, K. Giannitsas, A. Athanasopoulos
Journal: European Urology (2021)
Brown adipose tissue is associated with healthier body fat distribution and metabolic benefits independent of regional adiposity
Authors: Andreas G. Wibmer, Tobias Becher, Mahmoud Eljalby, Audrey Crane, Pamela Causa Andrieu, Caroline S. Jiang, Roger Vaughan, Heiko Schöder, Paul Cohen
Journal: Cell Reports Medicine (2021)

The association of brown adipose tissue (BAT) and body fat distribution and their combined effects on metabolic health in humans remains unknown. Here, we retrospectively identify individuals with and without BAT on 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography (PET)/computed tomography (CT) and assemble a propensity score-matched study cohort to compare body fat distribution and determine its role in mediating the benefits of brown fat. We find that BAT is associated with lower amounts of visceral adipose tissue and higher amounts of subcutaneous adipose tissue, resulting in less central obesity. In addition, BAT is independently associated with lower blood glucose and white blood cell count, improved lipids, lower prevalence of type 2 diabetes mellitus, and decreased liver fat accumulation. These observations are most prominent in individuals with central obesity. Our results support a role of BAT in protection from visceral adiposity and improved metabolic health.
Hormone treatment–related adverse events (HTR AEs) with darolutamide (DARO) in patients (pts) with nonmetastatic castration-resistant prostate cancer (nmCRPC) from the phase 3 ARAMIS study
Authors: K. Fizazi, N. Shore, M. Smith, J. Carles, T. Lebret, V. Lietuvietis, H. Mahammedi, A. Rannikko, E. Vjaters, P. Werbrouck, M. Miskic, I. Kuss, M. Le Berre, G. Borghesi, T. Sarapohja, S. Fayerabend
Journal: European Urology (2021)