tbuckley/cabot-search huggingface dataset:
Abstract 1453: Specific detection of mutant Ras oncoproteins in cell and tissue lysates by multiplex immunoassay
Authors: Joseph B. Hwang, Anthony Saporita, Qiang Xiao
Journal: Cancer Research (2020)

Abstract Ras proteins (HRAS, KRAS, and NRAS) are small GTPases that function as molecular switches by alternating between inactive GDP-bound and active GTP-bound states. Ras-GTP activates downstream pathways, including MAPK, by binding to Raf kinase and phosphatidylinositol 3-kinase (PI3K) to promote cellular proliferation, survival, growth and differentiation. Oncogenic mutations in Ras are found in approximately 25% of human cancers. Furthermore, 90% of pancreatic cancers harbor KRAS mutations with 80% of KRAS mutations occurring at codon 12 with G12V and G12D being the most prevalent. The Ras-Raf-MEK pathway can also be activated downstream of Ras. BRAF is a well-established oncogene, with the BRAF V600E mutation being prevalent in melanoma. While targeting this BRAF oncoprotein has had therapeutic efficacy, treating cancers driven by Ras oncoproteins remains an urgent unmet clinical need. We developed a novel multiplex immunoassay capable of simultaneously detecting total Ras, RasG12V, RasG12D, phospho-MEK1 (S217/S221), phospho-BRAF (S446) and phospho-CRAF (S338) in a single well. This multiplex assay detects the H-Ras, N-Ras, and K-Ras isoforms for total Ras, RasG12D, and RasG12V. To confirm specific recognition of mutant Ras oncoproteins, this kit was able to detect the known KRAS G12V mutation found in the COR-L23 cell line and the NRAS G12D mutation found in THP-1 cell line, respectively. In addition, the response to BRAF inhibitors vemurafenib and dabrafenib was compared between MDA-MB-435S cells, which harbor the BRAF V600E mutation, and insensitive cell lines, using multiplex immunoassays. While COR-L23 and THP-1 cells were not responsive to vemurafenib and dabrafenib, MDA-MB-435S cells showed a dramatic reduction in pMEK1 and pERK, consistent with inhibition of mutant BRAF protein. We then analyzed commercially-sourced tissue lysates, using tumor and adjacent tissue from a patient with colon cancer harboring a KRAS G12D mutation. While multiplex protein analysis revealed a similar phosphorylation pattern for Raf and MEK proteins, the RasG12D oncoprotein was specifically observed in lysate from the tumor but not the adjacent tissue. Finally, exosomes were enriched from pancreatic cancer serum and tested using the Ras-Raf Oncoprotein panel. These exosomal preparations yielded detectable signal for Total Ras and phospho-BRAF. Our data demonstrate the utility of studying the effects of Ras oncoproteins by multiplex immunoassay in multiple sample types, including cell, tissue, and exosomal lysates. Citation Format: Joseph B. Hwang, Anthony Saporita, Qiang Xiao. Specific detection of mutant Ras oncoproteins in cell and tissue lysates by multiplex immunoassay [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 1453.
Abstract 5247: Interleukin-11 could be a novel therapeutic target for lung adenocarcinoma patients
Authors: Laura Ojeda, Cristina Cirauqui, Sonia Molina-Pinelo, Eva M Garrido-Martín, Javier Ramos-Paradas, Patricia Yagüe, Alba Santos, Nuria Carrizo, Ana B. Enguita, Maria Teresa Muñoz, Jose Luis Solorzano, Luis Paz-Ares, Irene Ferrer
Journal: Cancer Research (2020)

Abstract Interleukin-11 (IL11) has been associated with tumorigenesis in a wide variety of tumors, including lung cancer, and it has been proposed as a diagnostic biomarker for lung adenocarcinoma. However, it is still not clear how IL11 affects the tumorigenesis. It is possible that, as other cytokines, it has a dual role in the tumor cell and tumoral microenvironment. Thus, the inhibition of IL11 could be an interesting therapeutic option to test in these patients. First, we confirmed the pro-tumorigenic effect of IL11 in patients and mouse models of lung adenocarcinoma (cancer cell lines xenografts, patient derived xenografts; PDXs and genetically engineered mouse models; GEMMs). Later, we knocked-down the expression of IL11 or its specific receptor IL11RA in adenocarcinoma cell lines in order to analyze their tumorigenic properties in vitro and in vivo. We confirmed that fibroblasts are a relevant source of IL11, so we knocked-down IL11 expression in order to analyze how it affects the fibroblasts´ properties, including the secretion of other pro-tumorigenic cytokines and growth factors. We reported that an increased expression of IL11 correlates with a poorer survival in lung adenocarcinoma patients and that IL11 stimulation increases the proliferation rates in xenografts, PDXs and GEMMs. On the contrary, IL11 or IL11RA knockdown in adenocarcinoma cell lines reduces their pro-tumorigenic properties in vitro and in vivo. Finally, the silencing of IL11 in fibroblasts reduces their proliferation, migration and secretion of pro-tumorigenic cytokines and growth factors. In conclusion, we propose that IL11 plays a direct pro-oncogenic role in lung adenocarcinoma tumoral cell and an indirect role in tumoral microenvironment. The genetic ablation of IL11 has an anti-tumoral effect, so it could be interesting to develop a pharmacological tool which neutralizes the IL11-IL11RA signaling to test as a therapeutic strategy in preclinical models. Thus, IL11 could represent a potential therapeutic target that deserves to be more exhaustively studied in the clinical settings. Citation Format: Laura Ojeda, Cristina Cirauqui, Sonia Molina-Pinelo, Eva M Garrido-Martín, Javier Ramos-Paradas, Patricia Yagüe, Alba Santos, Nuria Carrizo, Ana B. Enguita, Maria Teresa Muñoz, Jose Luis Solorzano, Luis Paz-Ares, Irene Ferrer. Interleukin-11 could be a novel therapeutic target for lung adenocarcinoma 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 5247.
Abstract LB-209: Integrative analysis of recurrent-metastatic progression in high-risk human papillomavirus cervical carcinomas
Authors: Youn Jin Choi, Yu Yeon Jung
Journal: Cancer Research (2020)

Abstract Purpose: The acquisition of recurrent/metastatic potential by a tumor cell defines a critical step of malignant progression. However, the understanding of metastatic progression at the molecular level is scarce for cervical carcinomas (CES). Materials and Methods: In this study, we performed comprehensive genomic, transcriptomic and viral profiling of five pairs of primary (CES-P) and matched recurrent/metastatic tumors (CES-R/M) with high risk human papillomavirus. Results: Whole exome sequencing revealed mutation features of CES-R/M such as elevated mutation burdens and prevalent copy number alterations compared to their matched CES-P. A relative deficit of APOBEC-related mutation signatures accompanying the transcriptional down-regulation of APOBEC3A was also observed for CES-R/M. Mutations on genes encoding epigenetic regulators were also commonly observed as CES-R/M-specific alterations. Immunoprofiling and gene set analysis further revealed that CES-P were enriched with transcripts representing activated anticancer immunity such as cytolytic scores and interferon-gamma pathway but CES-R/M showed the up-regulation of genes involved in epithelial-mesenchymal transition and angiogenesis. Viral capture sequencing also revealed the hotspots of viral integration such as 12q13. Moreover, we found that the transcriptional upregulation of POSTN and downregulation of APOBEC3A were associated with unfavorable clinical outcomes in CES. Conclusions: The comprehensive genomic and transcriptomic profiling of a rare cohort including CES-R/M identified metastases-specific features to advance the molecular understanding into the CES metastatic progression with potential clinical implication. Citation Format: Youn Jin Choi, Yu Yeon Jung. Integrative analysis of recurrent-metastatic progression in high-risk human papillomavirus cervical carcinomas [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-209.
Abstract 4084: A DGKA-cJUN-WEE1 signaling axis provides platinum resistance in ovarian cancer
Authors: Jie Li, Chaoyun Pan, Austin C. Boese, Anna Umano, Sumin Kang
Journal: Cancer Research (2020)

Abstract Although platinum compounds are the first-line treatment for ovarian cancer, the majority of patients relapse and develop resistance to treatment. However, the mechanism underlying resistance is unclear. Here, we report a unique platinum resistance mechanism that is mediated by a lipid messenger, phosphatidic acid (PA), in ovarian cancer. A phospho-proteomics screen revealed that PA, which is predominantly produced by diacylglycerol kinase alpha (DGKA) in ovarian cancer, activates the transcription factor c-JUN. DGKA and PA facilitate JNK recruitment to c-JUN and nuclear localization leading to its activation upon cisplatin exposure. Through a genomic screen, we identified that activated c-JUN enhances expression of WEE1 and consequently prevents cells from aberrant cell cycle progression upon cisplatin exposure. DGKA-cJUN-WEE1 signaling was elevated in tumors derived from ovarian cancer patients who did not respond to platinum-based therapy compared to tumors from patients who responded to treatment. Our study demonstrates how lipid metabolism, kinase signaling, and gene regulatory systems are intertwined to direct cisplatin resistance in ovarian cancer. Citation Format: Jie Li, Chaoyun Pan, Austin C. Boese, Anna Umano, Sumin Kang. A DGKA-cJUN-WEE1 signaling axis provides platinum resistance in ovarian 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 4084.
Abstract 6499: Small slide, big world: Fast detection of altered proteins and RNA levels in clinical samples using Nanostring nCounter® GeoMxTM Digital Spatial Profiler
Authors: Jingjing Gong, Matthew R. Farren, Walid Shaib, Gregory Lesinski, Sarah Warren, Yan Liang
Journal: Cancer Research (2020)

Abstract Although many new drugs have been approved and more clinical trials are being conducted for various disease therapies in recent decades, efficient identification of reliable therapeutic targets is still a big challenge during drug development. Therefore, tremendous efforts have been put into advancing the technology to quickly determine the altered biomarkers in clinical samples. Nanostring nCounter GeoMxTM Digital Spatial Profiling (GeoMx DSP) has been used in multiple projects and exhibited its outstanding performance on collecting analyzable digital counts for up-to 96 proteins and 20,000 RNAs in a specific area on a single FFPE slide. Tissue regions of interests are identified by fluorescent staining of morphology markers, and either proteins or RNAs in the specific defined regions are collected as the digital nCounter count format. By using this state-of-art technology, spatial distributions of immune- and cancer- relevant proteins were identified in 71 tumor cell rich-, 70 immune cell rich-, and 69 stromal cell rich- area respectively in three Pancreatic cancer patient groups including surgery alone, neoadjuvant FOLFIRINOX (a combination of fluorouracil, folinic acid, irinotecan and oxaliplatin) alone or combined with stereotactic body radiation therapy (F+SBRT). Our results showed that differential regulations among immune checkpoint markers, pan-immune markers and tumor markers in these treatment groups. In tumor-rich regions, CD44 is present at higher levels in FOLFIRINOX treated patients than surgery-alone group. VISTA was significantly down-regulated in F+SBRT group. Also, several key factors from pStat3, PTEN and Bcl2 pathways are also regulated by treatment methods. In immune-rich regions, both T cells markers (CD3 and CD4) and B cell markers (CD19 and CD20) were regulated differently by treatment methods. GeoMx DSP platform provides a novel and more precise view of the spatial regulation of micro-world in the tissue, which enable us to explore more about internal regulation within sub-population of the tissue cells. GeoMxTM DSP platform is only for RESEARCH USE ONLY. Not for use in diagnostic procedures. Citation Format: Jingjing Gong, Matthew R. Farren, Walid Shaib, Gregory Lesinski, Sarah Warren, Yan Liang. Small slide, big world: Fast detection of altered proteins and RNA levels in clinical samples using Nanostring nCounter® GeoMxTM Digital Spatial Profiler [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 6499.
Abstract 2750: An efficient multiplexing approach to avoid batch effects in single cell RNA- and Ab-seq studies demonstrated in a mouse model of chronic inflammation and obesity
Authors: Hye-Won Song, Gisele Baracho, Ian Taylor, Stephanie Widmann, Stefanie Mortimer
Journal: Cancer Research (2020)

Abstract Obesity can weaken the body's immune system and reduce its ability to fight off infections. Current analysis on immune cells from obese mouse models suggests that the immune cells suffer from chronic inflammation. To understand the root cause of this problem, we used single cell sequencing to examine thousands of immune cells isolated from primary and secondary lymphoid organs as well as adipose tissue and compared a diet-induced obesity mouse model with control mice. Cells were stained with 30 BD® AbSeq DNA-barcoded antibodies to enable multiomic analysis, i.e. examining protein alongside mRNA expression in tandem. We also utilized DNA-barcoded universal antibodies from the BD® Single-Cell Multiplexing Kit, which allowed us to combine 8 samples from different mice and tissue types into a single pooled sample, significantly reducing experimental scale and cost while eliminating potential batch effects. The pooled samples were loaded on the BD Rhapsody™ system to perform cell lysis and individual mRNA and cell barcoding, allowing measurement of ~400 immune-related mRNAs and 30 proteins at the single cell level. We were able to efficiently de-multiplex the pooled samples after sequencing. The targeted mRNA and AbSeq panel provided robust clustering of immune cell types and showed that genes related to critical immune responses, including inflammation and lymphocyte activation, are differentially regulated in specific immune-cell subsets in the obese mouse model. Using this multiomic analysis of genes differentially regulated in immune cells from different tissues, we propose a model to explain the immuno-phenotype we observed in obese mouse. For Research Use Only. Not for use in diagnostic or therapeutic procedures. BD, the BD Logo, and Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2019 BD. All rights reserved. Citation Format: Hye-Won Song, Gisele Baracho, Ian Taylor, Stephanie Widmann, Stefanie Mortimer. An efficient multiplexing approach to avoid batch effects in single cell RNA- and Ab-seq studies demonstrated in a mouse model of chronic inflammation and obesity [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 2750.
Abstract LB-015: Yap reprograms de novo lipogenesis to fuel liver cancer
Authors: Talhah M. Salmi, Srimayee Vaidyanathan, Malcolm J. McConville, Kristin K. Brown, Andrew G. Cox
Journal: Cancer Research (2020)

Abstract Hepatocellular carcinoma (HCC) is the most common form of liver cancer, originating from liver cells known as hepatocytes. At the molecular level, HCC is driven by transcription factors which are able to reprogram metabolism to support tumorigenesis that are still poorly understood. The Yes-associated protein (Yap) is the nuclear effector of the Hippo pathway, responsible in regulating organ size control and metabolism. Metabolic reprogramming has recently emerged as a fundamental hallmark of cancer. In our previous studies, we found that Yap integrates the anabolic demands of tumour growth by reprogramming glutamine and glucose metabolism to support nucleotide biosynthesis. The central aim of this study was to determine the role that Yap plays in regulating lipid metabolism in the context of liver cancer. We took advantage of a larval zebrafish model in which a hyperactivated form of Yap is specifically expressed in hepatocytes (lf:YapS87A;lf:NLS-mcherry). We found that the expression of Yap was sufficient to stimulate de novo lipogenesis (DNL) and induce lipid droplet formation in hepatocytes (steatosis). To determine whether the stimulation of DNL was required for oncogenic growth, we exposed larvae to pharmacological inhibitors of DNL and examined the impact on growth at the cellular level by multiphoton microscopy. Strikingly, we identified that fatty acid synthase (FAS) and stearoyl-CoA desaturase (SCD) inhibitors suppressed Yap-driven growth. To complement these studies, we took a genetic approach using CRISPR to generate FAS and SCD KO zebrafish larvae and we found that Yap-driven growth required both FAS and SCD. Importantly both chemical and genetic suppression of FAS and SCD activity had no effect on normal liver growth. Together, these findings suggest that oncogenic Yap-driven growth is conditionally dependent upon the stimulation of DNL. Consequently, these studies provide a rationale for examining the clinical efficacy of DNL inhibitors to combat liver cancer. Citation Format: Talhah M. Salmi, Srimayee Vaidyanathan, Malcolm J. McConville, Kristin K. Brown, Andrew G. Cox. Yap reprograms de novo lipogenesis to fuel liver 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 LB-015.
Abstract 6636: Therapy with BXCL701 (B), a DPP8, DPP9, DPPIV and FAP inhibitor, in combination with anti-PD1 antibody (PD1) in a syngeneic murine pancreatic ductal adenocarcinoma (PDAC) model improves treatment outcomes and induces intratumoral NK cell infiltrates and a marked reduction in tumor stromal fibrosis
Authors: Shangzi Wang, Allison Fitzgerald, Reham Ajina, Sandra A. Jablonsk, Louis M. Weiner, John MacDougall, Veena Agarwal, Vince J. O'Neill
Journal: Cancer Research (2020)

Abstract PDAC is typically resistant to chemotherapy and immunotherapy; therefore, novel strategies are needed to enhance therapeutic response. BXCL701 is a well-studied inhibitor of dipeptidyl peptidases 4, 8, 9, and Fibroblast Activation Protein, and has been postulated to work through cytokine induction and macrophage pyroptosis. We examined the effects of BXCL701 and/or PD1 therapy in murine models of PDAC. In the mT3-2D PDAC model, combination therapy of established (~75mm3) sc tumors reduced tumor growth to a greater extent (PBS: 1349±230 mm3 on day 42 vs B + PD1: 355±161mm3, p&amp;lt;0.0001) following a 28-day treatment program of PBS, B (1mg/kg by daily oral gavage), PD1 (10mg/kg ip weekly) or the combination of B + PD1. Treatment with either B or PD1 alone had minimal anti-tumor effects. B + PD1 therapy was accompanied by significant tumor infiltration of NK cells by IHC, flow cytometry and Nanostring analysis. A dramatic reduction of tumor stromal fibrosis by Masson's trichrome staining was found in tumors treated with B alone or B + PD1. These findings suggest that the combination of BXCL701 with anti-PD1 antibody therapy can exert anti-tumor effects associated with increased intratumoral NK cell content and the loss of fibrosis that may facilitate immunotherapy efficacy. Citation Format: Shangzi Wang, Allison Fitzgerald, Reham Ajina, Sandra A. Jablonsk, Louis M. Weiner, John MacDougall, Veena Agarwal, Vince J. O'Neill. Therapy with BXCL701 (B), a DPP8, DPP9, DPPIV and FAP inhibitor, in combination with anti-PD1 antibody (PD1) in a syngeneic murine pancreatic ductal adenocarcinoma (PDAC) model improves treatment outcomes and induces intratumoral NK cell infiltrates and a marked reduction in tumor stromal fibrosis [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 6636.
Abstract 5139: An atlas of perturbed functional proteomics profiles of cancer cell lines
Authors: Wei Zhao, Jun Li, Mei-Ju Chen, Rehan Akbani, Yiling Lu, Gordon Mills, Han Liang
Journal: Cancer Research (2020)

Abstract In recent years, tremendous efforts have been made to systematically characterize the molecular profiles of tumor tissues from individuals with cancer, laying a critical foundation for elucidating the molecular basis of tumorigenesis and developing biomarker-based diagnostic, prognostic and therapeutic approaches. In particular, cancer genomic data at the DNA or RNA level are being accumulated at an unprecedented speed. However, it remains to be a big challenge in cancer research to systematically understand causality and mechanisms underlying the behaviors of cancer cells. To address it, perturbation experiments are a very powerful approach in which the cells are first modulated by perturbagens and the downstream consequences are then monitored. Recently, large-scale compendia of the phenotypic and cellular effects of perturbed cancer cell lines have been established. However, similar resources for the proteomic responses of perturbed cancer cell lines have yet to be established. Reverse-phase protein arrays (RPPAs) is a powerful targeted functional proteomics approach to studying cancer mechanisms, biomarkers and therapies. This quantitative antibody-based assay is able to assess a large number of protein markers in many samples in a cost-effective, sensitive manner. More recently, we have applied this technology to quantify the protein expression levels of large patient cohorts and cancer cell lines (&amp;gt;8,000 patient samples of 32 cancer types from The Cancer Genome Atlas, &amp;gt;650 cell lines across 19 lineages). Here, using RPPAs, we have generated and compiled the perturbed functional proteomic profiles of &amp;gt;12,000 cancer cell line samples in response to &amp;gt;150 drug compounds and other perturbagens using reverse-phase protein arrays. We show that integrating protein response signals substantially increases the predictive power for drug sensitivity and gains insights into the mechanisms of drug resistance. We build a comprehensive map of “protein-drug” connectivity and develop an open-access, user-friendly data portal for community use. Our study provides a valuable proteomic resource for a broad range of quantitative modeling and biomedical applications. Citation Format: Wei Zhao, Jun Li, Mei-Ju Chen, Rehan Akbani, Yiling Lu, Gordon Mills, Han Liang. An atlas of perturbed functional proteomics profiles of cancer cell lines [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 5139.