tbuckley/cabot-search huggingface dataset:
Abstract 2507: Understanding endometrial cancer heterogeneity at single-cell resolution
Authors: Enrique I. Velazquez Villarreal, John D. Carpten, David W. Craig
Journal: Cancer Research (2020)

Abstract Endometrial cancer is the fourth most common gynecologic malignancy in the US. Tumor- associated genetic signatures are known to be associated with poorer prognosis of patients with endometrial cancer. In general, frequent gene alterations are enrichments of p53 and KRAS, PTEN, PIK3CA and PI3K/AKT mutations with variable CNV. Considerable evidence for intratumor heterogeneity indicate that bulk genomic sequencing approaches may be insufficient since endometrial cancer is characterized by extensive tumor heterogeneity. Here, to get new insight about endometrial cancer heterogeneity, we applied single cell sequencing since it has the potential to improve our understanding of this genetic feature by providing clonotype and variant information in high resolution. We examined cancer heterogeneity using single cell DNA sequencing Copy Number Variation (sc-DNAseq-CNV) analysis and clonotype detection in three tumors from patients with endometrial cancer. The technology used for processing single cell was 10x ChromiumTM Technology that provides detection of 100 Kb CNV events, calling clonotypes down to 10 of 1000 cell inputs. By processing these samples resulted in the sequencing of around 800 cells. Genome-wide ploidy analysis of the tumor cells showed variable median ploidies per sample. The regional copy number was estimated by processing our data in 20 Kb cases of reads. Multiple sub-clones were identified per sample number one where four clusters of sub-clones characterized cancer heterogeneity. Copy number changes on entire chromosome arms and mutations at variant detection level were detected since the resolution provided by single cell technology applied. Among the variant detection we identified previously reported mutations in POLE, POLE2, TP53, FGFR2, ARID1A, CTNNBI, PIK3CA, PIK3RI, KRAS and SWI/SNF in specific sub clones. Our study addresses the predominant challenge to determine tumor heterogeneity by performing better approaches to detect genomic differences and identifying molecular signatures among women with endometrial cancer. Better understanding of tumor heterogeneity may benefit patients diagnosed with endometrial cancer, or patients with specific molecular characteristics linked to endometrial cancer. Citation Format: Enrique I. Velazquez Villarreal, John D. Carpten, David W. Craig. Understanding endometrial cancer heterogeneity at single-cell resolution [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 2507.
An Important Role for DNMT3A-Mediated DNA Methylation in Cardiomyocyte Metabolism and Contractility
Authors: Alexandra Madsen, Grit Höppner, Julia Krause, Marc N. Hirt, Sandra D. Laufer, Michaela Schweizer, Wilson Lek Wen Tan, Diogo Mosqueira, Chukwuemeka George Anene-Nzelu, Ives Lim, Roger S.Y. Foo, Thomas Eschenhagen, Justus Stenzig
Journal: Circulation (2020)

DNA methylation acts as a mechanism of gene transcription regulation. It has recently gained attention as a possible therapeutic target in cardiac hypertrophy and heart failure. However, its exact role in cardiomyocytes remains controversial. Thus, we knocked out the main de novo DNA methyltransferase in cardiomyocytes, DNMT3A, in human induced pluripotent stem cells. Functional consequences of DNA methylation-deficiency under control and stress conditions were then assessed in human engineered heart tissue from knockout human induced pluripotent stem cell-derived cardiomyocytes.DNMT3A was knocked out in human induced pluripotent stem cells by CRISPR/Cas9gene editing. Fibrin-based engineered heart tissue was generated from knockout and control human induced pluripotent stem cell-derived cardiomyocytes. Development and baseline contractility were analyzed by video-optical recording. Engineered heart tissue was subjected to different stress protocols, including serum starvation, serum variation, and restrictive feeding. Molecular, histological, and ultrastructural analyses were performed afterward.Knockout of DNMT3A in human cardiomyocytes had three main consequences for cardiomyocyte morphology and function: (1) Gene expression changes of contractile proteins such as higher atrial gene expression and lower MYH7/MYH6 ratio correlated with different contraction kinetics in knockout versus wild-type; (2) Aberrant activation of the glucose/lipid metabolism regulator peroxisome proliferator-activated receptor gamma was associated with accumulation of lipid vacuoles within knockout cardiomyocytes; (3) Hypoxia-inducible factor 1α protein instability was associated with impaired glucose metabolism and lower glycolytic enzyme expression, rendering knockout-engineered heart tissue sensitive to metabolic stress such as serum withdrawal and restrictive feeding.The results suggest an important role of DNA methylation in the normal homeostasis of cardiomyocytes and during cardiac stress, which could make it an interesting target for cardiac therapy.
Abstract 4495: DNA demethylation promotes ERV expression and activation of immune signaling in renal cell cancer cells
Authors: Aguirre A. de Cubas, William Dunker, Rachel Hongo, Anuj Bhatia, Andrew Zaninovich, Anshuman Panda, Kathryn E. Beckermann, Gyan Bhanot, Shridar Ganesan, John Karijolich, W K. Rathmell
Journal: Cancer Research (2020)

Abstract Recently, we reported that expression of endogenous retroviruses (ERVs), a class of transposable element, is associated with response to immune checkpoint blockade (ICB) in renal cell carcinoma (RCC). Aberrant expression of ERVs can activate host antiviral responses, as well as produce neoantigens. ERV expression is repressed by DNA methylation and can be activated by DNA hypomethylating agents. Here, we investigate whether Decitabine, a DNA hypomethylating agent, can activate ERV expression and host antiviral defenses in RCC to potentially enhance response to ICB. Decitabine induced expression of ERV3-2 and ERV4700 in RCC cells lines, which was accompanied by activation of host antiviral defense genes and increased secretion of inflammatory cytokines. We validated this effect in primary human RCC cell lines. Knockout of RIG-I and MDA5 dsRNA sensors attenuated activation of antiviral responses associated with Decitabine treatment, and RIG-I and MDA5 immunoprecipitations showed increased ERV binding in RCC cells treated with Decitabine. Bioinformatic analysis of RNAseq data showed the Decitabine-induced gene signature could be associated with increased CD8 infiltration and response to ICB. Conditioned media from Decitabine treated RCC cells was capable of inducing host anti-viral defense in naïve RCC cells and could modestly improve activation of T-cells from healthy donors. Further, conditioned media from RCC cells treated with Decitabine significantly enhanced T-cell migration. In a small retrospective cohort of metastatic RCC patients treated with single-agent PD-1/PD-L1 blockade, activation of some host antiviral defense genes was significantly higher in responders compared with nonresponders. Thus, modulation of ERV expression by Decitabine to activate host antiviral defenses could represent a novel therapeutic strategy to enhance RCC patient response to immune checkpoint blockade. Citation Format: Aguirre A. de Cubas, William Dunker, Rachel Hongo, Anuj Bhatia, Andrew Zaninovich, Anshuman Panda, Kathryn E. Beckermann, Gyan Bhanot, Shridar Ganesan, John Karijolich, W K. Rathmell. DNA demethylation promotes ERV expression and activation of immune signaling in renal cell cancer 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 4495.
Abstract 3226: Facilitating personalized medicine with cloud-based storage and analytics
Authors: Rachel Howard, Kevin Hicks, Jamie Teer, Phillip Reisman, Mandy O'Leary, Steven Eschrich, Ross Mitchell, Howard McLeod, Dana Rollison
Journal: Cancer Research (2020)

Abstract The vast wealth of medical data collected over the last decade holds great promise for accelerating novel research, discovery, and clinical translation. Specifically, the rapid expansion of genomic testing provides new opportunities for the clinical management of cancer patients, influencing diagnosis, risk stratification, and treatment planning. Moffitt Cancer Center's Personalized Medicine Clinical Service integrates next-generation sequencing test results into patient care, using the data to guide individualized treatment plans. To maximize the efficiency and efficacy of this service, creative solutions for data harmonization, storage, and management are required. We implemented a commercial molecular data warehouse (MDW), directly linked to our existing clinical data warehouse, to store and manage molecular data ranging from genotypic alterations to annotations from public resources (HUGO, COSMIC, Ensembl) and clinically actionable targets (4,256 records currently loaded). A centralized, cloud-based data and analytics platform is also being implemented at Moffitt that will integrate a broad range of multi-modal data. In the cloud environment, the data from the MDW will be linked to typically siloed data streams from the electronic health record, cancer registry management system, biospecimen management system, billing and scheduling systems, patient-reported information and outcomes, and patient-generated health data, creating a unique and customized Personalized Medicine Curated Data Mart (CDM). In addition to describing the features of the MDW and the challenges faced during its implementation, we will provide an overview of the extensive data cleaning and curation required to facilitate such a CDM. This includes the extraction of disease characteristics from unstructured clinical text via natural language processing, creation of new derived data fields, approaches to extracting and managing complex treatment data, and the inclusion of detailed, manually-abstracted recurrence and outcomes data for historical patients from existing institutional datasets such as the Clinical Genomics Action Committee (CGAC) database. Finally, we will present prototypes of analytics dashboards that will interface directly with our CDM, facilitating intuitive data exploration for all members of our personalized medicine teams. Citation Format: Rachel Howard, Kevin Hicks, Jamie Teer, Phillip Reisman, Mandy O'Leary, Steven Eschrich, Ross Mitchell, Howard McLeod, Dana Rollison. Facilitating personalized medicine with cloud-based storage and analytics [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 3226.
Association of Urinary Matrix Metalloproteinase 7 Levels With Incident Renal Flare in Lupus Nephritis
Authors: Guobao Wang, Liling Wu, Huanjuan Su, Xiaodan Feng, Meng Shi, Lingwei Jin, Manqiu Yang, Zhanmei Zhou, Cailing Su, Bihui Yang, Yajing Li, Wei Cao
Journal: Arthritis & Rheumatology (2020)

Objective Flares of lupus nephritis (LN) are frequent and associated with impaired renal prognosis. One major management obstacle in LN flare is the lack of effective methods to identify at‐risk patients earlier in their disease course. This study was undertaken to test the utility of measurement of urinary matrix metalloproteinase 7 (MMP‐7) for the dynamic surveillance of renal disease activity and prediction of renal flares in LN. Methods A prospective, 2‐stage cohort study was performed in patients with LN. Urinary MMP‐7 levels at the time of biopsy were evaluated in 154 patients with newly diagnosed LN in 2 independent cohorts. Urinary MMP‐7 levels were assessed for correlation with renal histologic activity. Furthermore, after a minimum period of 12 months of renal disease remission, urinary MMP‐7 levels were monitored bimonthly for 2 years in 65 patients with LN. The association between urinary MMP‐7 levels and development of LN flare was analyzed. Results Urinary MMP‐7 levels were elevated in patients with LN. A higher urinary MMP‐7 level in LN was associated with greater renal histologic activity. As a marker for identifying LN patients with more severe renal histologic activity (i.e., a histologic activity index of ≥7), the level of urinary MMP‐7 outperformed other clinical markers and improved their predictive performance, thus linking urinary MMP‐7 levels to renal disease activity. Furthermore, among patients who had follow‐up measurements of urinary MMP‐7 after achievement of long‐term remission of renal disease activity, an elevated urinary MMP‐7 level during follow‐up was independently associated with an increased risk of LN flare. This elevation in the urinary MMP‐7 level hinted at the risk of an LN flare at an earlier time point prior to indications using conventional laboratory measures. Thus, use of the urinary MMP‐7 level in conjunction with other clinical measures improved the prognostic value for prediction of an LN flare. Conclusion Urinary MMP‐7 levels in LN are correlated with renal histologic activity. An elevated urinary MMP‐7 level detected after achievement of long‐term renal disease remission is associated with a higher risk of incident renal flare in patients with LN.
Abstract 5374: Rapid microfluidic isolation and detection of circulating tumor cells/clusters with zero sample preparation
Authors: Jian Zhou, Bin Liu, Qiyue Luan, Apurva Mallisetty, Alicia Hulbert, Ian Papautsky
Journal: Cancer Research (2020)

Abstract Background: Circulating tumor cells (CTCs) and clusters of liquid biopsy permits continual access to phenotypic and genotypic landscape of primary and metastatic tumors for optimized personalized therapy. In addition, it holds the promise of deciphering the tumor heterogeneity which is one of the major sources of treatment resistance. Due to the extreme rarity of CTCs in peripheral blood, rapid and reliable isolation remains challenging amid new technologies being tested. Herein, we developed and demonstrated a novel microfluidic approach capable of direct isolation of CTCs and clusters from untreated whole blood within 20 min. Methods: Our microfluidic approach takes advantages of the intrinsic strong cell-cell interactions when whole blood flows in a microchannel, which leads to faster lateral migration of larger cells and thus label-free isolation of CTCs based on size. Our biochip integrates cell isolation and cell immobilization units and allows processing of untreated whole blood at high throughput (2 mL in 20 min). Immobilized CTCs and clusters were subsequently characterized onchip by immunocytochemistry as CD45-, CK+ and DAPI+. Results: Blood samples of 9 deidentified patients diagnosed with non-small-cell-lung cancer (NSCLC) were directly processed through our microfluidic biochip. 2 mL whole blood of each sample were used without pretreatment. Immunofluorescence assay identified at least 1 CTC in the blood samples from all patients (100%). CTC count ≥ 5 was found in 8/9 samples (89%). The median of CTC count was 9 per 2 mL blood. A maximum of 38 CTCs per 2 mL whole blood was found in the sample of a late stage patient. Grape-like CTC cluster was also detected in one of the nine samples (11%). Conclusions: These “proof of concept” results suggest that our novel, label-free microfluidic technology is capable of rapid isolation and detection of CTCs and clusters directly from patient peripheral blood without sample pretreatment. It completely spares the need of costly, time-consuming and laborious sample pretreatment required by other methods. Further validation studies with cases and controls using patient lung tumor compared to the obtained CTC from our microfluidic approach are required before its implementation in the real-world practice. Citation Format: Jian Zhou, Bin Liu, Qiyue Luan, Apurva Mallisetty, Alicia Hulbert, Ian Papautsky. Rapid microfluidic isolation and detection of circulating tumor cells/clusters with zero sample preparation [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 5374.
Abstract 835: Novel framework for quantifying synergy in high-throughput drug combination cytotoxicity experiments
Authors: Robert Thurman, Bill Arthur
Journal: Cancer Research (2020)

Abstract Combination therapies are a cornerstone of cancer treatment, enabling a strategy of engaging multiple mechanisms of action. The in vitro testing of drug combinations is therefore a key step in drug discovery, and plate-based assays and robotics now allow for high-throughput cytotoxicity experiments that test combinations at doses diluted at high resolution. While additivity models such as Bliss, Loewe and Highest Single Agent (HSA) are well-established for gauging the synergy or antagonism of combinations, new frameworks are required for incorporating these models in the context of hundreds of experiments testing dozens of dose combinations per experiment. We have developed a framework that compares observed cytotoxicity results against the predictions from additivity models on a dose-by-dose basis across an entire matrix of dose combinations. Visualizations readily highlight any synergistic or antagonistic deviations from additivity. Statistical tests are then performed using 3x3 blocks of adjacent combinations. Such an approach mutes the effects of outliers and rewards consistency of activity in nearby doses. To capture the overall trend in an experiment and to facilitate comparisons across multiple experiments, we propose a summary metric, TSDA (total significant deviation from additivity) that takes into account both the absolute deviations from additivity and their statistical significance. Generally, positive values of TSDA indicate overall synergy, while negative values indicate overall antagonism. Null distributions for TSDA have been generated using simulations of sham experiments (same drug for both axes in a combination). We have applied this framework to over 1500 individual combination experiments spanning a range of cell lines and therapeutic mechanisms. The framework has been used to successfully guide follow-up in vivo experiments and to inform clinical plans. Citation Format: Robert Thurman, Bill Arthur. Novel framework for quantifying synergy in high-throughput drug combination cytotoxicity experiments [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 835.
Alignment and mapping methodology influence transcript abundance estimation
Authors: Avi Srivastava, Laraib Malik, Hirak Sarkar, Mohsen Zakeri, Fatemeh Almodaresi, Charlotte Soneson, Michael I. Love, Carl Kingsford, Rob Patro
Journal: Genome biology (2020)

Abstract Background The accuracy of transcript quantification using RNA-seq data depends on many factors, such as the choice of alignment or mapping method and the quantification model being adopted. While the choice of quantification model has been shown to be important, considerably less attention has been given to comparing the effect of various read alignment approaches on quantification accuracy. Results We investigate the influence of mapping and alignment on the accuracy of transcript quantification in both simulated and experimental data, as well as the effect on subsequent differential expression analysis. We observe that, even when the quantification model itself is held fixed, the effect of choosing a different alignment methodology, or aligning reads using different parameters, on quantification estimates can sometimes be large and can affect downstream differential expression analyses as well. These effects can go unnoticed when assessment is focused too heavily on simulated data, where the alignment task is often simpler than in experimentally acquired samples. We also introduce a new alignment methodology, called selective alignment, to overcome the shortcomings of lightweight approaches without incurring the computational cost of traditional alignment. Conclusion We observe that, on experimental datasets, the performance of lightweight mapping and alignment-based approaches varies significantly, and highlight some of the underlying factors. We show this variation both in terms of quantification and downstream differential expression analysis. In all comparisons, we also show the improved performance of our proposed selective alignment method and suggest best practices for performing RNA-seq quantification.
Abstract 1002: Immune microenvironment features of lung adenomatous premalignancy in a Chinese cohort
Authors: Liting Guo, Weiwei Shao
Journal: Cancer Research (2020)

Abstract Introduction: The widespread of implementation of computed tomography (CT) has resulted in a drastic increase in the detection of small pulmonary nodules presenting as ground glass opacities (GGOs). Many of these GGOs are atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), and sometimes invasive adenocarcinoma (IAC). The concept of a continuum between the precursor lesions AAH and AIS to MIA and frankly invasive IAC is backed by a wealth of recent data showing a gradual decrease in overall survival from 100% for AAH, AIS and MIA to moderately lower rates for IAC. A growing body of evidence suggests that the immune response is a significant determinant of cancer progression. However, little is known about the immune microenvironment features in the early stages of lung carcinogenesis. Methods: A total of 40 tumor tissue samples including 10 AAH, 10 AIS, 10 MIA and 10 early IAC from 40 patients who underwent surgical resection of pulmonary nodules at Yancheng No.1 People's Hospital, China were included. Immunohistochemistry (IHC) staining for the expression of CD3, CD4, CD8 and programmed death ligand 1 (PD-L1) to assess the role of T-cell immune surveillance in these pre- and early lung cancers were performed. Results: We observed CD3, CD4, CD8 and PD-L1 positivity in AAH, AIS, MIA and IAC, suggesting that immunoediting has started before the invasion. Higher expressions of CD3, CD4, CD8 and PD-L1 in IAC implying tumor invasion. Conclusions: Our preliminary results of the immune subgroups provide evidence for immune recognition in pulmonary premalignancy and are critical for understanding tumorigenesis and the development of effective preventive and interception strategies. Associations with genomic landscape is underway. Citation Format: Liting Guo, Weiwei Shao. Immune microenvironment features of lung adenomatous premalignancy in a Chinese cohort [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 1002.