tbuckley/cabot-search huggingface dataset:
Abstract 1247: Identifying novel regulators of the Unfolded Protein Response (UPR) by genome-scale CRISPR-Cas9 knockout screens
Authors: Nektaria Maria Leli, Souvik Dey, Lauren Brady, Constantinos Koumenis
Journal: Cancer Research (2017)

Abstract Development and growth of a tumor as well as its ability to metastasize involves a complex relationship with its tissue microenvironment. A proliferating tumor encounters several microenvironmental stress conditions such as hypoxia, lack of nutrients and acidosis. To cope with these conditions, cancer cells have developed elaborate cytoprotective mechanisms which provide them with distinct advantages to thrive. Thus, deciphering the signaling pathways which get activated in the tumor microenvironment has been paramount to develop new therapeutic strategies for treatment. The Unfolded Protein Response (UPR) is an adaptive prosurvival pathway elicited by stresses in the tumor microenvironment (e.g., hypoxia, low glucose) and involves translational and transcriptional activation of effector genes which act to relieve cellular stress and block cancer cell death. We developed a strategy to comprehensively analyze critical mediators of cell fate in response to UPR activation. We have delivered a lentiviral genome-scale CRISPR Cas9 knockout (GeCKOv2) library to Sq20B cells (human squamous head and neck carcinoma) and A375 (human melanoma) cells. The library is targeting 19,050 genes with 123,411 unique guide sequences and enables both negative and positive selection screening. We used the GeCKO v2 library to identify genes essential for triggering the UPR in response to thapsigargin and tunicamycin, known specific activators of ER stress. Our highest-ranking candidates include BIRC5/Survivin, a well-studied molecule that acts as an inhibitor of apoptosis and is highly expressed in cancer cells and eukaryotic translation initiation factor eIF6, whose overexpression increases motility and invasiveness of cancer cells. Our preliminary results indicate that loss of Survivin and eIF6 dramatically enhance sensitization of cells to various ER stress conditions. Moreover, this synergistic outcome is observed when cells are treated with YM155, a small molecule that selectively suppresses Survivin and is used in phase I/II clinical trials. Lastly, morphological changes like endoreduplication are observed after long term absence of Survivin indicating its endogenous ER stress inducing role. Taken together, Survivin and eIF6 are important mediators of survival following ER stress and characterizing the pathways involved can lead to the development of novel targeted agents and therapeutic approaches. Citation Format: Nektaria Maria Leli, Souvik Dey, Lauren Brady, Constantinos Koumenis. Identifying novel regulators of the Unfolded Protein Response (UPR) by genome-scale CRISPR-Cas9 knockout screens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1247. doi:10.1158/1538-7445.AM2017-1247
Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children
Authors: Hao Chung The, Paola Florez de Sessions, Song Jie, Duy Pham Thanh, Corinne N. Thompson, Chau Nguyen Ngoc Minh, Collins Wenhan Chu, Tuan-Anh Tran, Nicholas R. Thomson, Guy E. Thwaites, Maia A. Rabaa, Martin Hibberd, Stephen Baker
Journal: Gut Microbes (2017)

Diarrheal diseases remain the second most common cause of mortality in young children in developing countries. Efforts have been made to explore the impact of diarrhea on bacterial communities in the human gut, but a thorough understanding has been impeded by inadequate resolution in bacterial identification and the examination of only few etiological agents. Here, by profiling an extended region of the 16S rRNA gene in the fecal microbiome, we aimed to elucidate the nature of gut microbiome perturbations during the early phase of infectious diarrhea caused by various etiological agents in Vietnamese children. Fecal samples from 145 diarrheal cases with a confirmed infectious etiology before antimicrobial therapy and 54 control subjects were analyzed. We found that the diarrheal fecal microbiota could be robustly categorized into 4 microbial configurations that either generally resembled or were highly divergent from a healthy state. Factors such as age, nutritional status, breastfeeding, and the etiology of the infection were significantly associated with these microbial community structures. We observed a consistent elevation of Fusobacterium mortiferum, Escherichia, and oral microorganisms in all diarrheal fecal microbiome configurations, proposing similar mechanistic interactions, even in the absence of global dysbiosis. We additionally found that Bifidobacterium pseudocatenulatum was significantly depleted during dysenteric diarrhea regardless of the etiological agent, suggesting that further investigations into the use of this species as a dysentery-orientated probiotic therapy are warranted. Our findings contribute to the understanding of the complex influence of infectious diarrhea on gut microbiome and identify new opportunities for therapeutic interventions.
Abstract 4988: Genome-wide CRISPR screen and metabolite profiling reveal a new mechanism of methotrexate sensitivity
Authors: Naama Kanarek, Elizaveta Freinkman, Jason Cantor, Monther Abu-Remaileh, Tim Wang, David M. Sabatini
Journal: Cancer Research (2017)

Abstract The chemotherapeutic drug methotrexate (MTX) inhibits nucleotide biosynthesis and causes cell death by blocking DNA and RNA production. While MTX has had tremendous success as an anti-cancer treatment and is the subject of nearly a thousand ongoing clinical trials, we do not fully understand why certain cancers are more sensitive to it and why resistance emerges. To study these questions, we used a CRISPR-based genetic screen to identify genes that confer sensitivity to MTX. We identified an enzyme that plays a key role in a metabolic pathway that was not known to be associated with MTX sensitivity. Inhibition of the pathway, either by genetic loss of several genes in the pathway or through nutritional modulations, causes dramatic resistance to MTX in cultured cancer cells. Our results improved our understanding of the cellular response to MTX, and suggest that expression levels of enzymes in the pathway may serve as clinical predictor for MTX response in patients. Citation Format: Naama Kanarek, Elizaveta Freinkman, Jason Cantor, Monther Abu-Remaileh, Tim Wang, David M. Sabatini. Genome-wide CRISPR screen and metabolite profiling reveal a new mechanism of methotrexate sensitivity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4988. doi:10.1158/1538-7445.AM2017-4988
Abstract 1188: Sodium phenylbutyrate has an antineoplastic effect and enhances the cytotoxicity of 5-fluorouracil and irinotecan in colorectal cancer cell lines
Authors: Maha Al-Keilani, Ruba Darweesh
Journal: Cancer Research (2017)

Abstract Colorectal cancer is the third most common cancer in the world and it is the second leading cause of cancer-related deaths in the United States. About 25% of colorectal cancer cases present with metastases at time of diagnosis and 50% of patients who undergo surgery will ultimately develop metastatic disease. Consequently, adjuvant chemotherapy is required in many cases and it aims to prevent tumor progression and metastasis. Resistance to chemotherapy is the biggest obstacle in the treatment path of advanced colorectal cancer. Thus, highlighting the urgent need for the identification of new therapeutic agents that can enhance the cytotoxicity of the currently approved anticancer drugs. Sodium phenylbutyrate (NaPB), a salt of a short chain fatty acid that is used for treatment of urea cycle disorders, is under investigation for its antineoplastic potential. NaPB acts as a histone deacetylase inhibitor and it has been shown to be associated with reduced ER stress and enhanced JNK signaling pathway. This indicates that NaPB may enhance the cytotoxicity of the currently approved agents for colorectal cancer including oxaliplatin, 5-fluorouracil, and irinotecan. The aims of this study were to identify the antineoplastic potential of NaPB in colorectal cell lines, and to identify its effect on the cytotoxicity of oxaliplatin, 5-fluorouracil, and irinotecan. MTT proliferation assay showed that NaPB possessed a concentration dependent killing effect against HCT-116 and HT-29 colorectal cancer cell line (IC50 values were 5 and 10 mM respectively). Moreover, at clinically achievable and nontoxic concentration (2.5 mM), NaPB showed a synergistic effect in HCT-116 on 5-fluorouracil (R=14.176, p=0.006), on irinotecan (R=53.86, p=0.0117), and on oxaliplatin (R=20, p=0.004), but resulted in extensive cytotoxicity when used at 5 mM and 10 mM. In HT-29 cells, NaPB at concentrations 5 mM and 10 mM, showed a synergistic effect on 5-fluorouracil (R=5.5, p&amp;lt;0.001; and R=125, p&amp;lt;0.001 respectively), on irinotecan (R=5.7, p=0.016; and R=21.3, p=0.018 respectively), and on oxaliplatin (R=2.4, p=0.003; and R=3, p=0.002 respectively). The addition of NaPB at concentration of 20 mM to the previous drugs resulted in profound cytotoxic effect toward HT-29 cells. As a conclusion, NaPB is a promising new adjuvant antineoplastic agent that can be used to enhance the cytotoxicity of 5-fluorouracil, irinotecan, and oxaliplatin in colorectal cancer. Citation Format: Maha Al-Keilani, Ruba Darweesh. Sodium phenylbutyrate has an antineoplastic effect and enhances the cytotoxicity of 5-fluorouracil and irinotecan in colorectal cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1188. doi:10.1158/1538-7445.AM2017-1188
Abstract 3208: AZD1775 modulates kinetochore component Wee1-CDC2 and NF-κB signaling as potential therapeutic targets in head and neck squamous cell carcinoma
Authors: Zhengbo Hu, Anthony Saleh, Jianghong Chen, Carlson Sophie, Yi An, Clavijo Paul, Ru Wang, Shaleeka Cornelius, Zhong Chen, Carter Van Waes
Journal: Cancer Research (2017)

Abstract Recent findings in The Cancer Genome Atlas (TCGA) analysis of head and neck squamous cell carcinomas (HNSCC) revealed frequent alterations affecting the cell cycle and NF-κB pathway, which are critically involved in cancer cell proliferation and survival. We hypothesized that common mechanism(s) could coordinate cell cycle and NF-κB cell survival signaling in HNSCC. Recently, we established an NF-κB β−lactamase reporter UM-SCC-1 cell line and performed genome-wide RNAi screening to explore this hypothesis. We identified genes involved in the cell cycle and related to components of the kinetochore that co-modulate NF-κB activity. Among these targets, WEE1 kinase is currently under investigation as a therapeutic target of inhibitor AZD1775 in HNSCC. We found that WEE1-CDC2 axis protein levels were higher in a panel of HNSCC lines than in normal human oral keratinocytes (HOK). To further investigate the potential cross-talk between WEE1 cell cycle regulation and NF-κB activation, we showed that treatment of HNSCC cells with AZD1775 decreased NF-κB transcriptional activation and decreased TNFα-induced phosphorylation of IKKs and RELA subunit. Furthermore, AZD1775 inhibited NF-κB regulated proteins modulating the cell cycle and survival, including p21, CyclinD1, BCL2 and BCL-XL. These changes also correlate with alteration in cell cycle and survival detected by flow cytometry, as tumor cells treated by AZD1775 exhibited increased G2/M phase and sub-G0 fragmented DNA, and decease in G1/S phases. WEE1 inhibitor AZD1775 inhibited tumor cell proliferation and colony formation in a dose-dependent manner, and exhibited combinatory effects with cisplatin chemotherapy in tumor xenografts. Thus, we identified the novel cross-talk between WEE1-CDC2 and NF-κB signaling, potentially implicating decreased NF-κB prosurvival signaling in the anti-tumor activity of Wee1 inhibitors. (Supported by NIDCD/NIH intramural projects ZIA-DC-000016, 73, and 74; NIDCD core facility: advanced imaging, ZIC DC000081). Citation Format: Zhengbo Hu, Anthony Saleh, Jianghong Chen, Carlson Sophie, Yi An, Clavijo Paul, Ru Wang, Shaleeka Cornelius, Zhong Chen, Carter Van Waes. AZD1775 modulates kinetochore component Wee1-CDC2 and NF-κB signaling as potential therapeutic targets in head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3208. doi:10.1158/1538-7445.AM2017-3208
Increased Total mtDNA Copy Number Cures Male Infertility Despite Unaltered mtDNA Mutation Load
Authors: Min Jiang, Timo Eino Sakari Kauppila, Elisa Motori, Xinping Li, Ilian Atanassov, Kat Folz-Donahue, Nina Anna Bonekamp, Sara Albarran-Gutierrez, James Bruce Stewart, Nils-Göran Larsson
Journal: Cell Metabolism (2017)
Abstract 472: Role of miRNAome deregulation in the pathogenesis of non-alcoholic steatohepatitis (NASH)-derived hepatocellular carcinoma
Authors: Juliana F. Ortega, Aline DeConti, Kostiantyn Dreval, Fernando S. Moreno, Frederick A. Beland, Igor P. Pogribny
Journal: Cancer Research (2017)

Abstract Recent epidemiological studies have attributed the growing incidence of liver cancer, including hepatocellular carcinoma (HCC), in the United States to NASH, an advanced form of non-alcoholic fatty liver disease. Elucidating the molecular pathways that lead to the development of NASH-derived HCC is critical not only for identifying early diagnostic biomarkers of the disease, but also for treatment and prevention. We have investigated the role of microRNAs (miRNAs) in the development of NASH-derived HCC by using a Stelic Animal Model (STAM) of liver carcinogenesis. Using Liver miFinder PCR arrays, we examined the miRNA profiles in the livers of STAM mice and identified 25 and 35 miRNAs that were differentially expressed at a NASH-fibrotic stage (12 weeks) and in full-fledged HCC (20 weeks), respectively. Among these differentially expressed miRNAs, 18 miRNAs were in common. Multi-algorithm target prediction analysis of the common differentially expressed miRNAs revealed the involvement of these miRNAs in the deregulation of major molecular processes associated with the development of HCC, including epithelial-mesenchymal transition, HCC stem cell activation, and the induction of the β-catenin/Wnt and Hippo signaling pathways. These findings were confirmed by a marked up-regulation of Yes-associated protein 1 (YAP1), the main effector of the Hippo-pathway, the activation of epithelial-mesenchymal transition, and an increased-expression of hepatic progenitor cell markers. In addition to the common differentially expressed miRNAs, 10 miRNAs, including 5 members of the polycistronic oncomir miR-17-92 cluster, were found to be over-expressed in only HCC. These results indicate the fundamental role of miRNAs in the development of NASH-associated HCC. This is evidenced by the early occurrence of miRNA alterations at the preneoplastic stage of liver carcinogenesis, the persistence of these changes in HCC, and the accumulation of additional miRNA alterations in HCC, and by the existence of a mechanistic link between miRNA alterations and deregulation key cancer-related pathways. Citation Format: Juliana F. Ortega, Aline DeConti, Kostiantyn Dreval, Fernando S. Moreno, Frederick A. Beland, Igor P. Pogribny. Role of miRNAome deregulation in the pathogenesis of non-alcoholic steatohepatitis (NASH)-derived hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 472. doi:10.1158/1538-7445.AM2017-472
Abstract LB-015: Dissecting TGF beta-induced lethal EMT in Kras-driven pancreatic cancer
Authors: Jie Su
Journal: Cancer Research (2017)

Abstract Pancreatic cancer, mostly pancreatic ductal adenocarcinoma (PDAC), is a devastating malignancy with an extremely poor prognosis. New insights are urgently needed into the tumorigenesis process and the tumor suppression mechanisms of pancreatic cancer. Genetic alterations in PDAC occur in a temporal sequence, usually initiating with activating mutations of the KRAS (~95%), and progressing by loss of tumor suppressors, including INK4A/ARF, TP53 and SMAD4/DPC4. Our recent work reveals that in mouse KrasG12D-driven PDAC cells, TGFβ induces a robust epithelial-to-mesenchymal transition (EMT) response, which leads to cell apoptosis. To determine the KrasG12D-dependent mechanism of priming pancreatic epithelial cells to be sensitive to TGFβ-induced lethal EMT, we utilize systematic approaches to integrate the transcriptome profile and Smad2/3 binding patterns to the genome to identify candidate mediators that regulate TGFβ-induced lethal EMT. To identify TGFβ gene response changes mediated by KrasG12D, we perform RNA-Seq analysis of inducible Tet-On KrasG12D pancreatic epithelial cells (PECs) treating with TGFβ or SB505124. Systematic analyses reveal that mutant KrasG12D, but not KrasWT, enables robust TGFβ gene responses of Snai1, Has2, Has3 and IL11. The massive induction of these genes is crucial for TGFβ-induced lethal EMT. Smad2/3 ChIP-Seq analysis reveals that transcription factor binding motifs of Rreb1 are specially associated with these KrasG12D-enhanced Smad2/3 binding sites. Furthermore, depletion of Rreb1 greatly impairs TGFβ-induced apoptosis. In summary, oncogenic KrasG12D drives a cell state change and sensitizes premalignant PECs to respond to TGFβ-induced lethal EMT. This function switch of TGFβ is potentially mediated through Kras-activated Rreb1 as a specific DNA binding partner of Smads. Citation Format: Jie Su. Mem. Dissecting TGF beta-induced lethal EMT in Kras-driven pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-015. doi:10.1158/1538-7445.AM2017-LB-015
Abstract 5193: Hafnium oxide nanoparticles (NBTXR3), a novel radiation enhancer achieves marked antitumor efficacy across five tumor types
Authors: Ping Zhang, Sonia Vivet, Sébastien Paris, Agnès Pottier
Journal: Cancer Research (2017)

Abstract NBTXR3 are hafnium oxide nanoparticles (NPs) used for a single intratumor administration as radioenhancer in combination with radiation therapy (RT) as part of multi-modality of cancer treatment. The size, shape and surface of the NPs have been designed to develop strong interactions with cancer cells - effective cell binding and uptake - and to persist within the tumor mass during the whole RT treatment. The high electron density of the NPs is responsible for an increased probability of interaction with incoming ionizing radiations (when compared to tumor tissues with low electron density) and an increased energy dose deposition within the cancer cells which results in an enhanced tumor destruction when compared to RT alone. NBTXR3 works similar to the physical mode of action of RT, it does not rely on any biological system or target and constantly amplifies the radiation dose deposition (“on/off” activation). Here we present the transferability of the approach from one type of cancer to the other evaluating (i) the feasibility of the intratumor injection (intratumor availability of NBTXR3 nanoparticles by Computed Tomography (CT) or µCT) and (ii), the antitumor efficacy of NBTXR3 exposed to radiation. NBTXR3 NPs demonstrated a good intratumor availability and persistence across all tested tumor models (epithelial or mesenchymal origin), including human PDX tumor models. Notably, in PAC-120 tumor model the persistence of NBTXR3 NPs within the tumor mass was observed for more than 50 days which is equivalent to the entire duration of RT treatment. The antitumor efficacy was systematically enhanced in terms of tumor growth delay for animals treated with NBTXR3 and exposed to RT when compared to RT alone. NBTXR3 is currently in clinical trials in seven cancer indications including: soft tissue sarcoma, head and neck (H&amp;N), liver, rectal and prostate. These preclinical studies support the rationale for the development of NBTXR3 across all cancer indications where radiation treatment is used. NBTXR3 intratumor availability and antitumor efficacyTumor modelX-ray sources (antitumor efficacy)CT or µCTSarcomaHT1080200kV, Ir192LPS80T3 (PDX)200kV, Co60xA673Co60ProstatePC3150kVxDU145200kVxPAC120 (PDX)xH&amp;NCAL33200kVxFaDu200kVxColorectalHCT116Ir192xLungNCI-H460-luc2200kVx Citation Format: Ping Zhang, Sonia Vivet, Sébastien Paris, Agnès Pottier. Hafnium oxide nanoparticles (NBTXR3), a novel radiation enhancer achieves marked antitumor efficacy across five tumor types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5193. doi:10.1158/1538-7445.AM2017-5193
Abstract 747: An improved fixative for histomorphology, recovery of nuclic acids and proteins
Authors: Stephen M. Hewitt, Joon-Yong Chung, Candice Perry, Kris Ylaya, William M-A Smith, Robert A. Star
Journal: Cancer Research (2017)

Abstract Neutral Buffered Formalin (NBF) has been the primary diagnostic fixative for histopathology for nearly a century. The limitations of NBF are well known, especially with reference to the analysis of RNA and proteins. Alternative fixatives have been proposed, but not been widely adopted. Recently, the US Environmental Protection Agency (EPA) classified formaldehyde as a carcinogen, further tilting the balance away from the continued use of NBF. We recently described a fixative based on 70% ethanol and phosphate buffered saline, called BE70. Using BE70 as the base fixative, we have developed a modular fixative in which different chemicals can be supplemented for “fit for purpose” applications. The addition of guanidinium salts to BE70 , termed BE70G results in a fixative in which both proteins and nucleic acids are improved in quantity and quality after extraction from the paraffin block. The guanidinium replaces non-freezable water, and prevents hydrolysis and oxidation of the biomolecules. Histomorphology is not disrupted at lower concentrations, with only alterations of hematoxylin intensity at higher concentrations. Studies are underway to evaluate the stability of RNA and protein in the tissue block as well as on cut sections. This fixative, BE70G has the potential to address a number of challenges facing the development of precision biomarkers, while preserving histomorphology, and improving the safety of pathology staff. Other formulations are currently being evaluated that may support applications for cytology and electron microscopy. The goal is a well characterized fixative, in which modifications to the chemistry are defined and can be applied to obtain the optimal pathology specimen for both histomorphologic and molecular analysis. Citation Format: Stephen M. Hewitt, Joon-Yong Chung, Candice Perry, Kris Ylaya, William M-A Smith, Robert A. Star. An improved fixative for histomorphology, recovery of nuclic acids and proteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 747. doi:10.1158/1538-7445.AM2017-747