tbuckley/cabot-search huggingface dataset:
Abstract 1788: A high-throughput chemical genetic screen reveals SALL4-induced metabolic vulnerabilities in cancer
Authors: Justin L. Tan, Feng Li, Joanna Z. Yeo, Kol Jia Yong, Mahmoud A. Bassal, Guo Hao Ng, May Yin Lee, Chung Yan Leong, Hong Kee Tan, Chan-Shuo Wu, Bee Hui Liu, Hon Man Chan, Zi Hui Tan, Yun Shen Chan, Siyu Wang, Zhi Han Lim, Tan Boon Toh, Lissa Hooi, Kia Ngee Low, Siming Ma, Nikki R. Kong, Alicia J. Stein, Yue Wu, Matan T. Thangavelu, Atsushi Suzuki, Giridharan Periyasamy, John M. Asara, Yock Young Dan, Glenn K. Bonney, Edward K. Chow, Guo-Dong Lu, Huck Hui Ng, Yoganathan Kanagasundaram, Siew Bee Ng, Wai Leong Tam, Li Chai, Daniel G. Tenen
Journal: Cancer Research (2020)

Abstract Transcription factors are important drivers of cancer but the development of therapeutics against these factors has had limited success. We developed a stringent high-throughput chemical genetic screening platform to identify compounds that target oncogenic transcription factor SALL4 dependency in liver cancer. The platform comprises SALL4 low- and high-expressing endogenous and engineered isogenic liver cancer cell lines. Unexpectedly, from screening 21,575 natural product extracts, the top hits were four oxidative phosphorylation inhibitors that selectively reduced SALL4-dependent cell viability. The ATP synthase inhibitor oligomycin suppressed SALL4-expressing cancer in lung and liver cancer cell culture models, and in patient-derived xenograft models of liver cancer. Oligomycin also synergized with sorafenib, the standard-of-care targeted therapy in liver cancer, to effectively suppress SALL4-driven tumorigenesis in vivo. When aberrantly expressed in cancer, SALL4 binds ~50% of mitochondrial genes, including many oxidative phosphorylation genes, to predominantly upregulate their expression. SALL4 upregulation also alters the levels of oxidative phosphorylation-related metabolites and functionally increases oxidative phosphorylation activity. Application of our endogenous/isogenic transcription factor-screening platform revealed a therapeutically actionable oxidative phosphorylation vulnerability in SALL4-expressing cancers. Citation Format: Justin L. Tan, Feng Li, Joanna Z. Yeo, Kol Jia Yong, Mahmoud A. Bassal, Guo Hao Ng, May Yin Lee, Chung Yan Leong, Hong Kee Tan, Chan-Shuo Wu, Bee Hui Liu, Hon Man Chan, Zi Hui Tan, Yun Shen Chan, Siyu Wang, Zhi Han Lim, Tan Boon Toh, Lissa Hooi, Kia Ngee Low, Siming Ma, Nikki R. Kong, Alicia J. Stein, Yue Wu, Matan T. Thangavelu, Atsushi Suzuki, Giridharan Periyasamy, John M. Asara, Yock Young Dan, Glenn K. Bonney, Edward K. Chow, Guo-Dong Lu, Huck Hui Ng, Yoganathan Kanagasundaram, Siew Bee Ng, Wai Leong Tam, Li Chai, Daniel G. Tenen. A high-throughput chemical genetic screen reveals SALL4-induced metabolic vulnerabilities in 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 1788.
Abstract 375: <i>In vivo</i> metabolic autofluorescence imaging of macrophage heterogeneity across normal and cancerous tissue
Authors: Tiffany Heaster, Karla Esbona, Paul M. Sondel, Melissa C. Skala
Journal: Cancer Research (2020)

Abstract Tissue microenvironmental conditions affect macrophage metabolism and function. However, standard methods to measure macrophage function require tissue dissociation (e.g. flow cytometry) or tissue fixation (e.g. immunohistochemistry), which remove the cells from their native microenvironment and prevent in vivo monitoring. Autofluorescence imaging enables non-invasive, dynamic imaging of cell metabolism in live, intact samples by measuring fluorescence from metabolic co-enzymes, NAD(P)H and FAD, naturally present in all cells. Here, we test autofluorescence imaging to assess macrophage function in vivo within normal skin and tumor microenvironments. Transgenic mice harboring a floxed mCherry fusion protein controlled by the Csf1r promoter were crossed with Lyz2-Cre mice to generate a model of mCherry-expressing macrophages. Multiphoton wavelength mixing was used to simultaneously image mCherry, NAD(P)H, and FAD fluorescence in spectrally distinct channels. NAD(P)H and FAD fluorescence intensities and lifetimes were quantified for tissue-resident macrophages in the mouse ear dermis and tumor-associated macrophages in Panc02 pancreatic tumors engrafted on the flank. Spatial distributions of macrophages were visualized at each tissue site. Dermal macrophages were predominantly localized around hair follicles in the ear, while tumor-associated macrophages were randomly distributed throughout the tumor. Co-localization of mCherry and FAD signal indicated high FAD intensities within macrophages across both tissues. Population density modeling of autofluorescence variables on a single cell level in each tissue site indicate metabolic heterogeneity of macrophages within normal and cancerous tissues. Immunofluorescence of standard macrophage markers (CD86/CD206) further characterize diversity in macrophage phenotypes across both tissue microenvironments. These studies demonstrate metabolic autofluorescence imaging as a novel non-invasive tool to assess tissue-specific macrophage metabolism at the single cell level in vivo. Ultimately, this imaging approach could provide insight on the role of macrophage plasticity in tumor growth and treatment response in vivo. Citation Format: Tiffany Heaster, Karla Esbona, Paul M. Sondel, Melissa C. Skala. In vivo metabolic autofluorescence imaging of macrophage heterogeneity across normal and cancerous tissue [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 375.
Abstract 5990: The potential role of artificial lactate influx in remodeling cancer-specific metabolism of colorectal cancer
Authors: Keun-Yeong Jeong
Journal: Cancer Research (2020)

Abstract Cancer cells have a specific metabolic pathway that produces a large quantity of lactate from glucose by abnormal aerobic glycolysis, it can provide a secondary path that meets the metabolic needs for persistent survival. Accordingly, regulating cancer-specific metabolism has important implications for the discovery of novel therapeutics. In this study, the possibility of an impact on colorectal cancer was investigated that focused on the remodeling of cancer-specific aerobic glycolysis by the artificial influx of lactate. Intracellular lactate levels were assessed in the colorectal cancer cells following lactate calcium salt treatment. Expression of lactate dehydrogenase and pyruvate dehydrogenase were confirmed to investigate the effect of the increased lactate influx. The nicotinamide adenine dinucleotide ratio and concentration of α-ketoglutarate were measured to confirm the tricarboxylic acid coupling. The tube formation and wound healing assay were performed as well as the expression of hypoxia-inducible factor-1α and vascular endothelial growth factor receptor to confirm the loss of malignancy. Xenograft animal models were established to evaluate the antitumor efficacy by monitoring changes in the tumor volume. We demonstrated that an artificial influx of lactate was increased in colon cancer cells under a hypoxic condition thereby reversible activation of lactate dehydrogenase reacting to lactate. Then, the conversion to pyruvate was promoted, and as a result of increased stimulation of pyruvate dehydrogenase, the tricarboxylic acid was coupled, showing an oxidative metabolism similar to normal cells. The malignancy of cancer cells was lost by undergoing remodeling of such cancer-specific, and a significant decrease in tumor growth was confirmed as a result of the anticancer effect of artificial lactate influx. These findings suggest the unique mechanisms in which the artificial influx of lactate would have anticancer effects by regulating cancer-specific aerobic glycolysis. Citation Format: Keun-Yeong Jeong. The potential role of artificial lactate influx in remodeling cancer-specific metabolism of 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 5990.
Abstract 1864: Generation of a triple-mutation (T790M/C797S/L858R) NSCLC cell line for relevant drug discovery and development
Authors: Huiying Ma, Peixue Li, Peiran Zhang, Fuyun Sun, Qing Lin
Journal: Cancer Research (2020)

Abstract Epidermal Growth Factor Receptor (EGFR) overexpression is observed in a large subset of patients with non-small-cell lung cancer (NSCLC) and correlated with poor prognosis. Current approved treatment for EGFR mutation-positive NSCLC has been revolutionized with three generations of EGFR tyrosine kinase inhibitors (TKIs): the first- and second-generation TKIs, such as gefitinib, erlotinib and afatinib, selectively targeting EGFR activating mutations existing in exon 19 and 21; and the third-generation EGFR-wild-type sparing, irreversible activating mutations/T790M inhibitor, osimertinib. Patients with somatic activating mutations in the EGFR gene have dramatic response initially, but would eventually develop resistance to these TKIs. One leading evidence of osimertinib resistance is mediated by occurrence of the point mutation C797S. There are no effective therapeutic strategies to overcome this triple-mutation (activating mutations/T790M/C797S) mediated resistance. Therefore, it is urged to develop new drug to target this particular mutant. There is still lack of triple-mutation in vitro model for the new generation drug discovery. In this study, a triple-mutation NSCLC model was generated in the NCI-H1975 lung cancer cell line, which harbors other naturally occurring EGFR genomic aberrations - double-mutation (T790M/L858R) - inherent in NSCLC. We utilized the CRISPR/Cas9 genome editing tool to target endogenous loci in human NSCLC cell line NCI-H1975 and created the intend point mutation, resulting in the triple mutation cell line (T790M/C797S/L858R). Further phenotypic analysis demonstrated that the triple-mutation cell line was resistant to the third generation inhibitors in contrast to the parental double-mutation cell line. This newly developed triple-mutation lung cancer cell line provided a very useful tool for oncology drug discovery for NSCLC. Citation Format: Huiying Ma, Peixue Li, Peiran Zhang, Fuyun Sun, Qing Lin. Generation of a triple-mutation (T790M/C797S/L858R) NSCLC cell line for relevant drug discovery and development [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 1864.
Abstract 2836: Expression of the DEK oncogene in breast cancer cells promotes M2 polarization of tumor associated macrophages
Authors: Miranda Shephard, Nicholas Pease, Lisa M. Privette Vinnedge
Journal: Cancer Research (2020)

Abstract Breast cancer is the second leading cause of cancer deaths among women. DEK is a known oncoprotein found to be highly expressed in more than 60% breast cancers and is found to be an independent marker of poor prognosis. However, the molecular mechanisms by which DEK promotes tumor progression are poorly understood. To elucidate the oncogenic functions of DEK, we performed RNA-seq analysis on isogenic Dek-knockout and complemented murine breast cancer cells, which indicated dysregulation of immune signaling. Among the target genes identified and confirmed was an upregulation of thymic stromal lymphopoietin (TSLP) in Dek expressing murine breast cancer cells. TSLP was previously shown by Han et al to amplify the alternative (M2) activation of macrophages. M2-like macrophages are tumor promoting, they recycle iron for cell growth and encourage tissue remodeling and repair activities like angiogenesis. To test the immune modulating functions of Dek-expressing breast cancer cells, we treated bone marrow derived macrophages (BMDM) with tumor cell conditioned media. We found that in vitro, Dek expressing cancer cells induced an M2-like polarization of macrophages, as determined by the expression of M2-associated genes, enhanced migration, and iron recycling phenotypes, which was accompanied by inhibited ERK1/2 signaling. We found this phenotypic trend to be true in vivo, as well. In sectioned mammary tumors from MMTV-RontgDek+/+ and MMTV-RontgDek−/− mice, we see lower levels of iron staining in Dek+/+ tumors than in Dek−/− tumors using Prussian blue staining that co-localized with F4/80 macrophage marker staining. This suggested that Dek expression in the tumors induced an iron recycling, M2-like phenotype in tumor associated macrophages. Furthermore, we observed increased TSLP expression and angiogenesis, as determined by CD31 staining, in Dek-expressing tumors in vivo. These findings suggest that tumor Dek expression may promote breast cancer progression by inducing M2-like macrophage polarization in a murine breast cancer model. Citation Format: Miranda Shephard, Nicholas Pease, Lisa M. Privette Vinnedge. Expression of the DEK oncogene in breast cancer cells promotes M2 polarization of tumor associated macrophages [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 2836.
Abstract 2720: The GPC3 metastasis suppressor induces the activation of p38 MAPK signaling pathway promoting dormancy at the secondary organ
Authors: Magali Delgado Pastore, Macarena Guereño, Ana C. Lugones, Maria G. Peters
Journal: Cancer Research (2020)

Abstract GPC3 is a proteoglycan involved in the control of proliferation and survival, which has been linked to cancer. In this respect, we previously demonstrated that normal breast tissues exhibit high levels of GPC3, while its expression is diminished in tumors. However, the role of the GPC3 downregulation in breast tumor progression and its molecular and cellular operational mechanisms are not fully understood. In this study we showed that GPC3 reverts the epithelial-to-mesenchymal transition (EMT) underwent by mammary tumor cells, blocks metastatic dissemination and induces dormancy at secondary site. Using genetically modified murine breast cancer cell sublines, we demonstrated that the phospho-Erk/phospho-p38 ratio is lower in GPC3 reexpressing cells, while p21, p27 and SOX2 levels are higher, suggesting a dormant phenotype. In vivo metastasis assays confirmed that GPC3 reexpressing cells reduce their metastatic ability. Interestingly, the presence of dormant cells was evidenced in the lungs of inoculated mice. Dormant cells could reactivate their proliferative capacity, remain viable as well as tumorigenic, but they reentered in dormancy upon reaching secondary site. We also proved that GPC3 inhibits metastasis through the p38 MAPK signaling pathway activation. The in vivo treatment with a pharmacological inhibitor of p38 induced an increase in cell invasion of orthotopic tumors reexpressing GPC3, as well as in spontaneous and experimental metastatic dissemination. In conclusion, our study shows that GPC3 returns mesenchymal-like breast cancer cells to an epithelial phenotype, impairing in vivo metastasis and inducing tumor dormancy through p38 MAPK signaling activation. These results help to identify the genetic determinants of dormancy and suggest the translational potential of research focusing in GPC3. Citation Format: Magali Delgado Pastore, Macarena Guereño, Ana C. Lugones, Maria G. Peters. The GPC3 metastasis suppressor induces the activation of p38 MAPK signaling pathway promoting dormancy at the secondary organ [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 2720.
Abstract 6450: Circulating hepsin as a novel serum biomarker in prostate cancer patients
Authors: John Beard, Sam Eddington, Noah Bowman, Adam Cole, Timothy O'Brien, Blake P. Johnson
Journal: Cancer Research (2020)

Abstract Hepsin, a type II transmembrane serine protease, is commonly overexpressed in a variety of epithelial cancers, where its overexpression and concurrent proteolytic activity correlate with tumor progression. Recent studies indicate that Hepsin undergoes activation via autocatalysis and subsequent ectodomain shedding, thus highlighting its potential as a serum-based biomarker. Using transgenic mouse models of prostate adenocarcinoma, Hepsin overexpression has previously been implicated in disease progression and, notably, metastases that are neuroendocrine in nature. Collectively, these findings led us to explore the potential diagnostic utility of Hepsin expression in prostate cancer progression, inclusive of metastatic variants. Here, we reanalyzed pre-existing, publicly available gene expression datasets (2 datasets, 326 patient samples), which revealed a significant upregulation of Hepsin gene expression in tumor tissue versus benign tissue and further pronounced upregulation in androgen-dependent and -independent metastatic lesions. To further examine the potential correlation of Hepsin overexpression to androgen-independence, we reanalyzed in vitro data comparing LNCaP parental versus androgen-independent LNCaP subclones. This analysis revealed a stepwise increase in Hepsin expression over the course of androgen deprivation, which was accompanied by a concomitant decrease in PSA expression. Lastly, to evaluate circulating hepsin protein levels as they occur in patient serum, a total of 424 subjects suspected of prostate cancer were analyzed for circulating Hepsin levels from 2015 to 2018 at the time of biopsy and followed for recurrence or survival until the end of the study. Serum Hepsin levels, as determined by enzyme-linked immunosorbent assay, rendered a specificity of 89% (Gleason &amp;lt; 6 (3+3); Hepsin positive, &amp;gt;100 ng/mL). Within this cohort, 18 patients presented with biochemical recurrence, of which 44% were Hepsin positive and exhibited a 22-month accelerated clinical path to recurrence versus Hepsin negative patients. Collectively, these results highlight the longitudinal diagnostic potential of circulating Hepsin levels in the prostate cancer setting. Citation Format: John Beard, Sam Eddington, Noah Bowman, Adam Cole, Timothy O'Brien, Blake P. Johnson. Circulating hepsin as a novel serum biomarker 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 6450.
A novel rationale for targeting FXI: Insights from the hemostatic microRNA targetome for emerging anticoagulant strategies
Authors: Jamie Nourse, Sven Danckwardt
Journal: Pharmacology & Therapeutics (2020)

Therapeutic targeting of blood coagulation is a challenging task as it interferes with the delicate balance of pro- and anticoagulant activities. Anticoagulants are employed in millions of thrombophilic patients worldwide each year. The treatment and prevention of venous thromboembolism has changed drastically. Traditional vitamin K antagonists are being replaced by direct oral anticoagulants (DOACs), which selectively target coagulation factors Xa or IIa. However for a growing population with comorbidities satisfying therapeutic options are still lacking and the quest for novel therapeutics continues. Recently, targeting factors XI or XII have emerged as new therapeutic strategies. As these factors play important roles in thrombosis, yet are essentially dispensable for hemostasis, these strategies may overcome the obstacle of treating or preventing thrombosis without affecting hemostasis. Based on the recent elucidation of the hemostatic microRNA targetome, we introduce and discuss a hitherto unrecognized rationale for the therapeutic targeting of factor XI. This is based on mimicking endogenous factor XI expression control by therapeutic delivery of microRNA mimics. We discuss the functional difference between various gene-targeting approaches, and propose the hemostatic system to represent an ideal model for assessment of the efficacy and safety of such therapeutic components, ushering in a novel therapeutic era with broad applicability.
Abstract 219: A high throughput single-cell workflow for paired genomic and phenotypic analysis
Authors: Dalia Dhingra, Pedro Mendez, Aik Ooi, Shu Wang, Saurabh Gulati, Adam Sciambi, Dave Ruff
Journal: Cancer Research (2020)

Abstract Fusion gene detection has long been a focus of cancer research, when combined with mutations found in gDNA, can lead to a better understanding of disease progression. One example, BCR-ABL, a marker for CML and AML stem cells, is a target for tyrosine kinase inhibitor (TKI) treatments; however, there are mutations within BCR-ABL that evade TKIs and are selectively resistant to drug therapy. Single-cell technologies are now able to provide information into genomic DNA content, RNA expression, and protein surface markers, unmasked by the heterogeneity found in bulk data. However, multimodal analysis from the same single cell has not been straightforward to implement in a high throughput single-cell workflow. Here, we report the development of chemistries that enable analyses of both targeted genomic DNA and RNA sequencing from the same cell. This workflow relies on the Tapestri platform, which uses a two-step microfluidic droplet system for the analysis of thousands of cells per run. The first droplet encapsulates each cell and releases the DNA while the second droplet introduces additional reagents for enzymatic manipulations on the cellular analytes. Novel primer designs are leveraged to capture both DNA and RNA and provide for independent barcoded sequence information. We first establish the utility of the Tapestri platform for accurate gene expression assessment with a targeted panel for breast cancer. For fusion gene transcript detection, panels were designed for AML and CML including primers targeting multiple potential variants of BCR-ABL transcripts. Cell lines were used to show high sensitivity and specificity of fusion sequence calls from RNA in cells where the expected SNVs, indels, and CNVs were also detected from gDNA. More complex targeted RNA and DNA panels, such as one for breast cancer with 35 gene expression amplicons and 88 genotyping amplicons, were also tested where we show agreement between cells clustered based on RNA expression and the cell assignment based on SNVs from gDNA. This single-cell multimodal workflow on the Tapestri platform currently has the power to quantitatively link genotypic and phenotypic data from the same cell with future potential in biomarker identification and ultimately, to link to best-fit therapeutics. Citation Format: Dalia Dhingra, Pedro Mendez, Aik Ooi, Shu Wang, Saurabh Gulati, Adam Sciambi, Dave Ruff. A high throughput single-cell workflow for paired genomic and phenotypic analysis [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 219.