tbuckley/cabot-search huggingface dataset:
Abstract 5702: A spatially resolved single cell atlas of the human breast
Authors: Tapsi Kumar, Quy Nguyen, Kevin Nee, Shanshan Bai, Min Hu, Emi Sei, Anita Wood, Jie Wiley, Hui Chen, Alejandro Contreras, Mediget Teshome, Ken Chen, Bora Lim, Devon Lawson, Nicholas Navin, Kai Kessenbrock
Journal: Cancer Research (2020)

Abstract The human breast consists of lobules connected to an intricate network of ducts that are surrounded by fatty tissues, designed to produce and transport milk to nourish offspring. Histopathology has identified 10 major cell types based on morphological features but have provided limited information on cell states - the transcriptional programs of cell types that reflect different biological functions. In this study we have generated an unbiased ‘cell atlas' of the normal human breast to define the cell types and cell states using single cell RNA sequencing and spatial transcriptomics methods. We performed 3' microdroplet based single cell and nuclei RNA sequencing of 248,687 stromal cells and 89,301 nuclei from 24 women with pathologically normal breast tissues that were collected from mastectomies and reduction mammoplasties. Unbiased expression analysis identified four major cell types: adipocytes, epithelial cells (luminal and basal), fibroblasts and endothelial cells and defined their transcriptional programs. Additionally, 8 minor cell types were identified in the breast, including macrophages, T-cells, natural killer cells, mast cells, pericytes, apocrine cells, neurons and smooth muscle cells. Our data revealed hundreds of novel markers of these cell types and defined their transcriptional programs and cell states. Most cell types had multiple transcriptional programs including luminal epithelial cells (hormone receptor positive and secretory), basal epithelial cells (myoepithelial or basal), endothelial cells (E1, E2, E3), myeloid cells, T-cells and fibroblasts (F1-F4) and provided insight into developmental lineages. We further delineated the spatial organization of these cell types and cell states within the tissue architecture using spatial transcriptomics assay. The breast cell atlas data provides an invaluable normal reference for the research community to understand how normal cell types are reprogrammed in diseases such as breast cancer. Citation Format: Tapsi Kumar, Quy Nguyen, Kevin Nee, Shanshan Bai, Min Hu, Emi Sei, Anita Wood, Jie Wiley, Hui Chen, Alejandro Contreras, Mediget Teshome, Ken Chen, Bora Lim, Devon Lawson, Nicholas Navin, Kai Kessenbrock. A spatially resolved single cell atlas of the human breast [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 5702.
Abstract 2228: PD1/CTLA4 humanized mice - A great model for pre-clinical toxicology and efficacy evaluation of macromolecular drugs
Authors: Cunxiang Ju, Mingkun Zhang, Rui Mao, Ma Xiuying, Jin Tang, Shuai Li, Jingjing Wang, Hongyan Sun, Jing Zhao, Xiang Gao
Journal: Cancer Research (2020)

Abstract Immune checkpoint antibodies have conferred huge cancer immunotherapeutic effect (CITE). Besides, severe immunotherapy related adverse events (irAE) occurred in combination therapy such as anti-PD1 combines with anti-CTLA4 antibodies greatly limit the development of cancer therapy. Animal models which can recapitulate both clinical irAE and CITE will be benefit for developing safer immune-checkpoint-targeting reagents. However, no animal models were found can be used for preclinical safety evaluation of drugs up to now. Given this fact, PD1/CTLA4 double-humanized mice models were established in both BALB/c (BALB/c-hPD1/hCTLA4) and C57BL/6 (B6-hPD1/hCTLA4) background, which by replacing the mouse extracellular domain of CTLA4 and PD1 with human segments while retaining mouse intact intracellular part, respectively. Our data showed that strong CITE against anti-hCTLA4 treatment observed in models from both BALB/c and B6 background. Apparent inhibition of tumor growth also emerged on subcutaneously engrafted CT26 tumor in BALB/c-hPD1/hCTLA4 mice by anti-PD1/CTLA4 bispecific antibody treatment. Meanwhile, severe irAEs which have been observed in clinical patients, such as joint swelling, skin inflammation, heart damage and infiltration of inflammatory cells in different tissues and organs could be reproduced in BALB/c-hPD1/hCTLA4 mice. Consistent with previous reports, we could not observe similar irAEs under drugs treatment at the same dose in C57BL/6-hPD1/hCTLA4 mice. Our data indicated that adult BALB/c-hPD1/hCTLA4 mice, but not C57BL/6-hPD1/hCTLA4 mice, were more sensitive to irAEs. Taken together, adult PD1/CTLA4 humanized mice in BALB/c background can not only be used to screen humanized antibodies, but also have tremendous values for preclinical safety evaluation. Citation Format: Cunxiang Ju, Mingkun Zhang, Rui Mao, Ma Xiuying, Jin Tang, Shuai Li, Jingjing Wang, Hongyan Sun, Jing Zhao, Xiang Gao. PD1/CTLA4 humanized mice - A great model for pre-clinical toxicology and efficacy evaluation of macromolecular drugs [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 2228.
Abstract 541: CLL-1 specific chimeric antigen receptor T cells (CART) as a novel AML therapy
Authors: Antonio Freitas, Anne-Sophie Gautron, Mayumi Sugita, Srinjoy Goswami, Roman Galetto, Andrew Garton, Julianne Smith, Agnes Gouble, Michael W. Becker, Gail J. Roboz, Monica L. Guzman
Journal: Cancer Research (2020)

Abstract Acute myeloid leukemia (AML) is a disease with high incidence of relapse that is originated and maintained from leukemia stem cells (LSCs). Hematopoietic stem cells (HSCs) can be distinguished from LSCs by an array of markers including CD123, CLL-1, amongst others. Thus, these are thought to be unique candidates to eliminate LSCs using a variety of targeted approaches, including chimeric antigen receptor (CAR) T cells. Here, we evaluated the potential of CLL-1 as a therapeutic target for LSCs using allogeneic gene-edited CAR T cells (UCARTCLL1). UCARTCLL1 cells are TCRαβneg human T cells derived from healthy donors, and expressing an anti-CLL-1 CAR under the control of the endogenous TRAC promoter. This is achieved following a 2-in-1 TRAC knock-out CAR knock-in strategy using TALEN® gene-editing technology. UCARTCLL1 cells are also knocked-out for the beta 2 microglobulin gene. We first assessed the expression of CLL-1 across samples from 41 AML patients and 4 healthy donors. The AML samples included 32 de novo and 9 relapse samples. Using multi-parameter flow cytometry, we evaluated CLL-1 expression on blasts and phenotypically defined leukemic stem cells (CD34pos CD38neg). We found that the majority of the blasts were positive for CLL-1. Furthermore, we found that 36 out of 41 primary AML samples had phenotypically defined stem cells (CD34pos CD38neg) from which 35 showed more than 0.1% CLL-1pos cells. Previous work has shown that individuals with more than 0.1% putative LSCs will have worse outcomes (Van Renhen et al). Thus, this data suggests that there is a subset of putative CLL-1 positive LSCs that if not eliminated by current therapies could lead to disease relapse. Therefore, we sought to determine the therapeutic potential of UCART cells targeting CLL-1. First, we evaluated cytotoxic efficacy of UCARTCLL1 cells at different effector to target ratios in 7 primary AML samples with different levels of CLL-1 expression. We observed a significant cytotoxic effect specific to the CLL1pos subsets. Notably, CLL-1pos cells in the AML samples treated with 5:1 and 1:1 ratios were completely eliminated. Currently, we are evaluating the in vivo activity of UCARTCLL1 cells in AML-PDX mouse models to determine their efficacy at eliminating AML blasts, progenitors and LSCs. Citation Format: Antonio Freitas, Anne-Sophie Gautron, Mayumi Sugita, Srinjoy Goswami, Roman Galetto, Andrew Garton, Julianne Smith, Agnes Gouble, Michael W. Becker, Gail J. Roboz, Monica L. Guzman. CLL-1 specific chimeric antigen receptor T cells (CART) as a novel AML therapy [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 541.
Abstract 2995: Dissecting renal cell carcinoma vulnerabilities: Using CRISPR/Cas9 to study resistance to glutaminase inhibition
Authors: Aleksandra M. Raczka, Paul A. Reynolds
Journal: Cancer Research (2020)

Abstract The aim of this study was to identify genes, which when knock out confer resistance to a novel glutaminase inhibitor in Renal Cell Carcinoma (RCC). RCC represents around 3% of all malignancies worldwide, with its most common type, clear cell RCC (ccRCC), making up around 70-80% of all RCC. The most frequent genomic alteration in ccRCC involves loss of VHL gene in &amp;gt;90% of ccRCC cases. Large-scale cancer genomics sequencing studies have identified several driver genes beyond VHL, particularly PBRM1 (40%), SETD2 (15%), and BAP1 (10%). RCC is characterised by significant tumour heterogeneity and inherent (in 25-30% cases) or acquired resistance to available chemotherapeutics. Glutamine addiction is a potential new therapeutic target for RCC as it has been recently shown not only to rely on glutamine for energy generation and maintenance of redox homeostasis, but also de novo pyrimidine synthesis. CB-839 is a small, orally administered reversible inhibitor of human kidney-type glutaminase (GLS). CB-839 is currently in early phase clinical trials and shows promising results. Given the significant incidence of resistance to previously approved therapies, we have applied a genome-scale CRISPR/Cas9 approach in a cell culture model of ccRCC (786-0 cell line) to identify candidate genes, which when knocked down confer resistance to CB-839. Next generation sequencing data analysis of drug-selected sgRNA library representation from two timepoints was performed using the MAGeCKFlute bioinformatics workflow. We conducted the screen in two biological replicates and verified successful genome-scale sgRNA library coverage at baseline in both cases. As a result, we identified candidate genes and pathways that are implicated in tumour metabolism, autophagy and metastasis. Additionally, this analysis identified KD genes, which in combination with CB-839 are synthetic lethal. We have prioritized the top 12 candidate genes, which we are validating in four cell lines (786-0, A498, A704 and Caki-1). After establishing CRISPR/Cas9 single gene knockdown (KD) cell lines, KD is confirmed using RT-qPCR and Western Blot, followed by functional analysis. KD cells were treated with increasing concentrations of the drug in parallel with a cell line containing a scrambled sgRNA to detect growth changes between the two. After in vitro validation, we performed ex vivo validation of the candidate hits. Our data show that the genome-scale CRISPR/Cas9 approach is effective in identifying candidates modulating drug resistance to CB-839. Citation Format: Aleksandra M. Raczka, Paul A. Reynolds. Dissecting renal cell carcinoma vulnerabilities: Using CRISPR/Cas9 to study resistance to glutaminase inhibition [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 2995.
Preoperative carfilzomib and lulizumab based desensitization prolongs graft survival in a sensitized non-human primate model
Authors: Paul M. Schroder, Robin Schmitz, Zachary W. Fitch, Brian Ezekian, Janghoon Yoon, Ashley Y. Choi, Miriam Manook, Andrew Barbas, Frank Leopardi, Mingqing Song, Alton B. Farris, Bradley Collins, Jean Kwun, Stuart J. Knechtle
Journal: Kidney International (2020)
Abstract 2109: Amplicon design algorithm for single cell targeted DNA sequencing using machine learning
Authors: Shu Wang, Saurabh Gulati, Dong Kim, Sombeet Sahu, Saurabh Parikh, Nianzhen Li, Manimozhi Manivannan, Nigel Beard
Journal: Cancer Research (2020)

Abstract Background: To realize the promise of precision medicine for cancer, assessing genetic variation present in rare cells and understanding the role that these cells play in the evolution of tumor progression is essential. High throughput single cell DNA targeted sequencing enables detection of rare mutations in cells and identification of subclones defined by co-occurrence of mutations. The big challenge with multiplex sequencing at single cell level is the non-uniform amplification of the targeted regions during PCR. This results in inadequate coverage of mutations of interest in the panel and hence makes genotyping challenging. To address this challenge, we developed a machine learning engine to optimize amplicon design for uniform amplification by making reliable performance prediction. Methods: Multiple panels with various sizes were designed with amplicons spanning a wide range of design properties such as amplicon GC, length, secondary structure prediction, primer specificity. These panels were synthesized and processed through Tapestri single cell DNA platform. The tested amplicons are classified into low-performer, OK-performer and high flyer based on their normalized reads-per-cell value. Design properties and property distribution of the amplicons and the panel are the features. We used random forest classifier to calculate feature importance and analyzed the range of the top features for each class and their significance of variance between classes. These ranges were then used as parameters in the assay design pipeline. Next, we train machine learning models with performance data to develop a performance prediction engine. Results: To test the performance of the design pipeline with new parameters, we designed a small (31), medium (128) and large (287) amplicon panel. Multiple runs were conducted for each panel with different cell types. We were able to achieve high panel performance of 97%, 92% and 88% across the three panels. The new parameters resulted in ~10-20% improvement in panel uniformity. We are working on further optimizing the performance prediction engine by using different ML classification models with K-fold cross validation, training using larger group of amplicons and optimizing features using combinations of properties. Citation Format: Shu Wang, Saurabh Gulati, Dong Kim, Sombeet Sahu, Saurabh Parikh, Nianzhen Li, Manimozhi Manivannan, Nigel Beard. Amplicon design algorithm for single cell targeted DNA sequencing using machine learning [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 2109.
Abstract LB-157: Obesity at early adulthood increases subsequent risk of gastric cancer in high incidence nation: Results from the Health Examinees-Gem (HEXA-G) study
Authors: Hwi-Won Lee, Woo-Kyoung Shin, Jae Jeong Yang, Minkyo Song, Aesun Shin, Jong-koo Lee, Daehee Kang
Journal: Cancer Research (2020)

Abstract Background: The global trend of obesity, or the “obesity epidemic,” is not confined to adults. The increasing rates of obesity at young age signifies potential burden to our society as a whole, and requires prompt attention. Although emerging evidence has indicated a possible link of obesity in early life to subsequent cancer risks, the association with gastric cancer remains largely unknown, especially among the populations with high incidence rates of gastric cancer. Objective: Using data from the Health Examinees (HEXA) study of Korea, this study aimed to investigate the association of obesity at younger age (ages 18-20 and 35) with the later risk of gastric cancer in a population with high incidence rate of gastric cancer. Method: Included were 114,155 cancer-free subjects who participated in the large-scale prospective cohort study of the Health Examinees-Gem (HEXA-G) study during 2004-2013. Multivariate Cox proportional hazards models were used to estimate hazard ratios (HR) and 95% confidence intervals (CI) for gastric cancer risk associated with body mass index (BMI) at age 18-20 and 35. To consider substantial differences in incidence rates between men and women, the overall associations were further evaluated, separately by sex. Results: During a median follow-up period of 6.2 years, 851 gastric cancer cases (476 men and 375 women) were identified. When compared to normal BMI (18.5 - 23.0kg/m2), obesity (BMI ≥30kg/m2) at age 35 was significantly associated with increased risk of gastric cancer later in life: HR (95% CI) = 2.60 (1.57-4.33) for total participants, 2.11 (1.03-4.34) for men, and 3.82 (1.86-7.86) for women. No significant associations were found for obesity at late adolescence in both men and women. Conclusion: Our findings suggest that obesity in early adulthood may be associated with increased risk of gastric cancer. Preventing obesity in early life may help reduce the health burden of gastric cancer in later life. Citation Format: Hwi-Won Lee, Woo-Kyoung Shin, Jae Jeong Yang, Minkyo Song, Aesun Shin, Jong-koo Lee, Daehee Kang. Obesity at early adulthood increases subsequent risk of gastric cancer in high incidence nation: Results from the Health Examinees-Gem (HEXA-G) study [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 LB-157.
Abstract 1580: Distinct pathways of lytic and blastic bone metastases in prostate cancer patients
Authors: Claire L. Ihle, Meredith D. Provera, Desiree M. Straign, E. Erin Smith, Susan M. Edgerton, Adrie Van Bokhoven, M. Scott Lucia, Philip Owens
Journal: Cancer Research (2020)

Abstract The most common metastatic lesions of prostate cancer are in the bone and can be classified into three distinct pathologic subtypes: lytic, blastic, and an indeterminate mixture of both. There is no immunotherapy guidance for treating patients based on lytic or blastic tumor induced bone disease. To identify distinct tumor and stroma in lytic and blastic prostate cancer bone metastases, we investigated a cohort of decalcified formalin-fixed and paraffin-embedded (FFPE) patient bone biopsy specimens that contained metastatic prostate cancer with lytic or blastic features. Tissue sections were utilized for immunohistochemistry (IHC) staining, isolation of RNA for gene expression, and Digital Spatial Profiling (DSP) of changes in both the tumor and microenvironment. A diverse set of unique immune cell populations and signaling pathways to both lytic and blastic types of prostate cancer metastases were present. High proportions of macrophages were present in lytic tumor induced bone disease, and T cells were present in lytic and blastic samples. In blastic lesions, immune cells were enriched for pSTAT3 and components of the JAK-STAT pathway. In lytic lesions, immune cells exhibited enhanced pAKT activity and components of the PI3K-AKT pathway. Expression of key immune checkpoint targets were identified in blastic prostate cancer, providing new therapeutic targets for patients with bone metastases. To further investigate which individual cells comprising the stroma and tumor have active JAK-STAT signaling, we performed fluorescent multiplex-IHC (mIHC). A tumor and myeloid panel of antibodies was used to identify on a single cell resolution which specific cell types are enriched for pSTAT3 in the tumor microenvironment. The identification of pAKT or pSTAT3 as promising therapeutic targets could be rationally employed to individual patients. The presence of macrophages and T cells in samples suggest that conventionally “cold” prostate cancer bone metastases warrant reappraisal as capable immunotherapy responders. Biopsies could guide selection of patients into appropriate therapeutic interventions based on protein levels and RNA expression of desired targets in metastatic disease. Citation Format: Claire L. Ihle, Meredith D. Provera, Desiree M. Straign, E. Erin Smith, Susan M. Edgerton, Adrie Van Bokhoven, M. Scott Lucia, Philip Owens. Distinct pathways of lytic and blastic bone metastases in prostate cancer patients [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 1580.
Covid-19: Government faces criticism over £500m plan to pilot mass testing
Authors: Gareth Iacobucci
Journal: BMJ (2020)

Experts have questioned the UK government's decision to expand its testing programme for covid-19 to the mass population, including people without symptoms.Current government advice is that only people with symptoms should have a covid-19 test.But on 3 September the government announced a substantial investment of £500m (€558m; $661m) to support trials of wider mass population testing, as well as a quicker "20 minute" saliva test for covid-19. 1 Jon Deeks, professor of biostatistics at the University of Birmingham and lead author of a recent Cochrane review of covid-19 antibody tests, questioned the wisdom of mass testing, given the potential for false positives."If you start testing everybody it turns into a screening programme, and you need to be very clear that you're going to do more good than harm by this," he said."With these tests, there's been a lot of concern about false positives.Experts on screening should be advising on this.