bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A32: The role of the ribosome in GCN2's ability to sense amino acid deprivation and initiate the integrated stress response
Authors: Inglis Alison J. , Shao Sichen , Masson Glenn R. , Perisic Olga , Hegde Ramanujan S. , Williams Roger L. 
Published: May 2017

Abstract
The ability to replicate without limit is one of the traditional hallmarks of cancer. It is therefore evident that the majority of tumor cells are operating in environments with limited nutrients. This means that tumor cells are disproportionately reliant on their stress response pathways in comparison to healthy cells. One such stress response pathway is a component of the integrated stress response pathway that responds to deprivation of amino acids. GCN2 is a serine/threonine protein kinase that is activated in response to a drop in the intracellular concentration of amino acids. Upon activation, GCN2 phosphorylates the translational initiation factor eIF2, inhibiting its activity in the translational cycle. This leads to a global inhibition of translation, whilst paradoxically upregulating the expression of certain genes involved in stress responses. It has been shown that knocking out GCN2 leads to a significant reduction in the growth of tumors in mice, suggesting that GCN2 could be a useful therapeutic target.
We have expressed and purified human GCN2 and found it to be a dimer, as has been observed for yeast GCN2. We have shown in vitro that GCN2 becomes autophosphorylated, and it catalyses phosphorylation of a putative binding partner GCN1 as well as eIF2. We have found that human GCN2 forms a stable complex with 80S ribosomes, and mammalian 80S ribosomes significantly increase GCN2 kinase activity in vitro, consistent with a previous report that an increase in ribosomal stalling leads to a rise in eIF2 phosphorylation in vivo. We are attempting to determine the structure of GCN2 bound to ribosomes in order to understand the detailed interactions and the molecular mechanisms that lead to GCN2 activation.
Citation Format: Alison J. Inglis, Sichen Shao, Glenn R. Masson, Olga Perisic, Ramanujan S. Hegde, Roger L. Williams. The role of the ribosome in GCN2's ability to sense amino acid deprivation and initiate the integrated stress response. [abstract]. In: Proceedings of the AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; 2016 Oct 27-30; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2017;77(6 Suppl):Abstract nr A32.
Abstract A33: Understanding the functional role of enhanced FASN activity in regulating protein translation in DLCBL
Authors: Kapadia Bandish , Gartenhaus Ronald 
Published: May 2017

Abstract
Fatty acid synthase (FASN) and protein translational machinery are two emerging cancer therapeutic targets, but their mutual dependency on each other for tumor growth especially in diffuse B-cell large lymphoma (DLBCL) is currently unknown. Therefore, we investigated the functional consequences of enhanced FASN activity on protein translational machinery in both DLCBL cell lines as well as primary samples. Inhibition of FASN activity by a specific inhibitor, C75 or shRNA mediated knockdown, suppressed de novo protein synthesis in SUDHL2, Pfeiffer, and HLY-1 cells, whereas SUDHL4 and SUDHL6 cells displayed minimal impact. Assessing the core translational machinery, the eif4b (eukaryotic initiation factor 4b) levels were depleted in a dose dependent manner of C75 treatment or shRNA mediated knock down of FASN. Mechanistically, eif4b undergoes ubiquitin mediated protein degradation upon FASN depletion. Importantly there seems to be a direct correlation between FASN levels and eif4b expression in DLBCL samples. Depleting the expression of eif4b significantly reduced the cell proliferative capacity of both FASN sensitive as well as resistant DLBCL cells. Screening the interacting protein partners from the available databases, we observed that USP11 interacts and deubiquitinates eif4b which increases its overall stability. Furthermore altering the expression of USP11 or its activity by either chemical inhibition or mutations significantly alters nascent peptide synthesis. Significantly, either down regulating USP11 or inhibiting via small molecules significantly reduced the cell proliferation with increased apoptosis of either FASN activity sensitive or resistant DLBCL cells. USP11 expression was also elevated in DLBCL tissues. Importantly, there is a strong correlation between USP11 and FASN as well as eif4b expression in DLBCL with higher level of this proteins associated with poorer survival. Enhanced FASN activity increased the Akt kinase activity, which phosphorylates USP11 at an evolutionary conserved site. FASN stimulated Akt-meditated phosphorylation events is critical for USP11 recruitment on translational initiation machinery as well as interaction with eif4b to alter protein biosynthesis. These results demonstrate that FASN mediated eif4b/USP11 axis is required for cell proliferation and survival by regulating the translation of proliferative and prosurvival mRNAs. Targeting the eif4b/USP11 axis for therapeutic intervention may add additional treatment options for resistant/relapsed DLBCL patients.
Citation Format: Bandish Kapadia, Ronald Gartenhaus. Understanding the functional role of enhanced FASN activity in regulating protein translation in DLCBL. [abstract]. In: Proceedings of the AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; 2016 Oct 27-30; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2017;77(6 Suppl):Abstract nr A33.
Abstract A40: Expression of cancer-associated fibroblast-related proteins differs between invasive lobular carcinoma and invasive ductal carcinoma
Authors: Eun-Sol Kim , Seung Koo Ja 
Published: May 2017

Abstract
Purpose: Cancer-associated fibroblasts (CAFs) are classified into various functional subtypes such as fibroblast activation protein-α (FAP-α), fibroblast specific protein-1 (FSP-1), platelet-derived growth factor receptor-α (PDGFR-α), and PDGFR-β. In this study, we compared the expression of CAF-related proteins in invasive lobular carcinoma (ILC) with those in invasive carcinoma of no special type (NST), and assessed the implications of the differences observed.
Methods: Using tissue microarrays of 104 ILC and 524 invasive carcinoma (NST) cases, immunohistochemistry for CAF-related proteins [podoplanin, prolyl 4-hydroxylase, FAP-α, FSP-1/S100A4, PDGFR-α, PDGFR-β, and chondroitin sulfate proteoglycan (NG2)] was conducted.
Results: In invasive carcinoma (NST), tumor cells expressed a high level of PDGFR-α, whereas ILC tumor cells expressed high levels of podoplanin, prolyl 4-hydroxylase, FAP-α, and FSP-1/S100A4. In stromal cells of invasive carcinoma (NST), high expression levels of prolyl 4-hydroxylase, PDGFR-α, and NG2 were observed, whereas ILC stromal cells expressed high levels of FAP-α, FSP-1/S100A4, and PDGFR-β. In ILC, tumoral FSP-1/S100A4 positivity was associated with higher Ki-67 labeling index (p = 0.010) and non-luminal A type cancer (p = 0.014). Stromal PDGFR-α positivity was associated with lymph node metastasis (p = 0.011). On survival analysis of entire cases, tumoral FSP-1/S100A4 positivity (p = 0.001) and stromal podoplanin positivity (p = 0.035) were associated with shorter disease-free survival; only tumoral FSP-1/S100A4 positivity (p = 0.001) was associated with shorter overall survival.
Conclusion: In ILC, the expression of FAP-α and FSP-1/S100A4 was higher in both tumor and stromal cells than that observed in invasive carcinoma (NST). These results indicate that CAFs are a potential target in ILC treatment.
Citation Format: Lee YuKyung, Kim Eun-Sol, Koo Ja Seung. Expression of cancer-associated fibroblast-related proteins differs between invasive lobular carcinoma and invasive ductal carcinoma. [abstract]. In: Proceedings of the AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; 2016 Oct 27-30; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2017;77(6 Suppl):Abstract nr A40.
Abstract B05: Characterization of the pre-ribosomal complex, which mediates the p53 Impaired Ribosome Biogenesis Checkpoint (IRBC)
Authors: Menoyo Sandra , Gentilella Antonio , Thomas George 
Published: May 2017

Abstract
Ribosome biogenesis is one of the most energy consuming anabolic processes in a growing tumor cell. For more than a century it has been recognized that the increased size and abnormal morphology of nucleoli, the sites of ribosome biogenesis, are markers of aggressive cancers, particularly sporadic colorectal cancers (sCRC). The TCGA has recently published that over 90% of sCRCs have a mutation in the WNT/APC signaling pathway, leading to persistent c-Myc activation in almost all cases. As c-Myc tumors are addicted to high rates of ribosome biogenesis, recent studies have suggested that impaired ribosome biogenesis, leading to the activation of p53 may serve as an Achilles' heel in the treatment of such tumors. Although a number of ribosomal proteins (RPs) have been implicated in inducing p53 stabilization following impaired ribosome biogenesis, our laboratory has shown that this response is mediated by a ribosomal precursor complex made-up of RPL5, RPL11 and non-coding 5S rRNA, which upon a lesion in ribosome biogenesis is redirected from assembly into nascent 60S ribosomal subunits to the binding and inhibition of Hdm2, leading to p53 stabilization, cell cycle arrest and apoptosis. We have termed this response the Impaired Ribosome Biogenesis Checkpoint (IRBC). However the sequence of molecular events that determine the transition of the RPL5/RPL11/5S rRNA-precursor complex upon impaired ribosome biogenesis into a tumor suppressor, the IRBC complex, are unknown. Here we present the use of a colon cancer cell line endogenously tagged by means of CRISPR/Cas9 with a GFP-fusion moiety placed at the eukaryotic-specific N-terminal extension of one copy of the gene coding for RPL11, which behaves as the wild type allele in terms of ribosome assembly and protein synthesis. We are using cells expressing this allele i) to follow by live imaging the endogenous IRBC complex localization over time under normal growing conditions or upon inducing lesions in ribosome biogenesis known to trigger the IRBC and p53 stabilization and (ii) to determine underlying molecular and biochemical alterations leading to the transition of the RPL5/RPL11/5S rRNA-precursor complex into of the IRBC complex.
Citation Format: Sandra Menoyo, Antonio Gentilella, George Thomas. Characterization of the pre-ribosomal complex, which mediates the p53 Impaired Ribosome Biogenesis Checkpoint (IRBC). [abstract]. In: Proceedings of the AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; 2016 Oct 27-30; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2017;77(6 Suppl):Abstract nr B05.
Abstract B39: Asparagine drives translational adaptation of cancer cells to glutamine deficit
Authors: Pavlova Natalya N. , Zhang Ji , Thompson Craig B. 
Published: May 2017

Abstract
Most proliferating cells consume exogenous glutamine to fuel biosynthesis and cell growth, which leads to its marked depletion from the microenvironment. Glutamine provides carbon and nitrogen for a wide array of biomolecules, among which are non-essential amino acids, glucosamine and nucleotides; in addition, carbon backbone of glutamine is used as a preferred anaplerotic input into the TCA cycle. However, as recent in vivo metabolomic studies indicate, a number of tumor types are capable of utilizing alternative anaplerotic routes and, in fact, synthesize glutamine de novo. In addition, select cancer cell lines are able to proliferate in the absence of exogenous glutamine in culture medium. However, the metabolic and regulatory underpinnings that enable the cellular adaptation to glutamine deficit and de novo glutamine production need further investigation.
In this work, we identified the non-essential amino acid asparagine as essential for the survival and proliferation of cancer cells in the absence of exogenous glutamine supply. Our data indicate that asparagine, though structurally related to glutamine, is not catabolized in the same manner. Instead, asparagine acts by restoring protein translation, which becomes profoundly compromised in the absence of glutamine. This, in turn, enables the post-transcriptional adaptive upregulation of glutamine synthetase (GLUL), which is required for glutamine-independent growth. Taken together, these findings show that the cellular adaptation to glutamine-limiting conditions relies upon the availability of asparagine, which may represent an important therapeutic vulnerability.
Citation Format: Natalya N. Pavlova, Ji Zhang, Craig B. Thompson. Asparagine drives translational adaptation of cancer cells to glutamine deficit. [abstract]. In: Proceedings of the AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; 2016 Oct 27-30; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2017;77(6 Suppl):Abstract nr B39.
Abstract IA14: Rare codons capacitate Kras-driven de novo tumorigenesis
Authors: Pershing Nicole L.K. , Lampson Benjamin L. , Counter Christopher M. 
Published: May 2017

Abstract
The KRAS gene is commonly mutated in human cancers, rendering the encoded small GTPase constitutively active and oncogenic. We discovered that this gene has the unusual feature of having a bias towards rare codons, which are associated with poor translation. Indeed, by changing rare codons to common the amount of KRAS mRNA detected in the heavy fraction by polysome profiling was reduced in lockstep with an increase in protein expression. This poor translation of KRAS has a direct impact on oncogenesis, but curiously, not in the direction one might expect. Specifically, we treated mice in which rare codons in the Kras gene were changed to common with a carcinogen known to induce lung tumors characterized by oncogenic Q61L/R mutations in Kras. Interestingly, these mice exhibited a reduction in tumor burden. Moreover, not only was the altered Kras allele mutated less often, but when it was mutated, completely different mutations were detected, namely G12V/D. We attribute this to a selection against the stronger Q61L/R mutations in favor of weaker G12V mutations in the higher expressed modified Kras allele, as strong oncogenic signaling leads to growth arrest instead of proliferation. As such, the poor translation of KRAS may reduce the chance that an oncogenic mutation induces growth arrest, which perhaps is related to the high frequency this gene is mutated in human cancers or even why specific KRAS mutations map to certain cancers.
Citation Format: Nicole L.K. Pershing, Benjamin L. Lampson, Christopher M. Counter. Rare codons capacitate Kras-driven de novo tumorigenesis. [abstract]. In: Proceedings of the AACR Special Conference on Translational Control of Cancer: A New Frontier in Cancer Biology and Therapy; 2016 Oct 27-30; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2017;77(6 Suppl):Abstract nr IA14.
Abstract IA12: Targeting DNA repair in cancer therapy
Authors: D'Andrea Alan D. 
Published: May 2017

Abstract
Human cancer cells have genomic instability resulting from germline or acquired defects in DNA repair. One DNA repair pathway—the Fanconi Anemia/BRCA pathway (D'Andrea, A., N Engl J Med 362:1909, 2010)—is defective in many human cancers, including breast, ovarian, and pancreatic neoplasms. Disruption of the FA/BRCA Pathway results in the characteristic chromosome instability and radiation/crosslinker hypersensitivity of these tumors. In general, loss of one DNA repair pathway often leads to hyperdependence on another pathway for tumor cell survival. This hyperdependence offers a unique opportunity for the development of anticancer therapeutics. For instance, FA/BRCA pathway deficient tumors are hyperdependent on Base Excision Repair (BER) and, accordingly, these tumors are hypersensitive to single agent treatment with PARP1 inhibitors, which block BER, or with ATM inhibitors. Our research program is focused on profiling the FA/BRCA pathway and the other five major DNA repair pathways in tumor cells (Kennedy and D'Andrea, JCO 24: 3799, 2006). Each DNA repair pathway has a characteristic biomarker and repairs a specific type of DNA lesion. By profiling these pathways in primary tumor samples with activation-specific antibodies to DNA repair proteins, we have been able (1) to predict the sensitivity of tumors to conventional chemotherapy and radiation (2) to subset tumors for their sensitivity to novel classes of DNA repair inhibitors, (i.e., PARP1, Chk1, ATM, and proteasome inhibitors) and (3) to screen for new small molecule inhibitors of other DNA repair pathways. This combination of novel DNA repair inhibitors, conventional DNA damaging agents, and DNA repair biomarkers offers new opportunities for developing more effective anticancer therapy. In my presentation, I will also discuss novel approaches to sensitizing Triple Negative Breast Cancers (TNBCs) and Ovarian Tumors (OCs) to PARP1 inhibitors. We have previously shown that exposure of these tumors to either a CDK inhibitor or a proteasome inhibitor can block homologous recombination (HR) repair and thereby sensitize the tumor cells to PARP1 inhibitor. The CDK inhibitor/PARP1 inhibitor combination has been examined in orthotopic primary TNBC and OC xenograft models. Finally, we have identified an additional PARP1-dependent DNA repair mechanism in TNBCs and OCs. This pathway is driven by a novel alternative end-joining polymerase, POLθ. These tumors are hypersensitive to inhibitors of this new pathway, suggesting a new target for DNA repair therapies.
Citation Format: Alan D. D'Andrea. Targeting DNA repair in cancer therapy. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Targeting the Vulnerabilities of Cancer; May 16-19, 2016; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(1_Suppl):Abstract nr IA12.
Abstract IA19: Novel insights into T cell recognition and regulation at the tumor site
Authors: Furness Andrew J. S. 
Published: May 2017

Abstract
Regulation of T cell function represents a key obstacle to the successful clinical application of tumor immunotherapy. Antibody-mediated blockade of co-inhibitory immune checkpoint molecules seeks to address such regulation. Durable remissions and even cure has been observed in patients with advanced cancer, however such responses are limited to a small fraction of treated patients. The identification of biomarkers predictive of response and resistance to therapy therefore remains an area of high scientific priority. Recent studies highlight the impact of the genomic landscape on anti-tumor immunity. Tumor-specific mutations may serve as neoantigens, eliciting T cell responses, and appear to be enriched in patients with advanced melanoma and non-small cell lung cancer (NSCLC) deriving benefit from CTLA-4 and PD-1 blockade respectively.
Genetic heterogeneity within single tumors is well described, however the impact of intra-tumor heterogeneity (ITH) upon the neoantigen landscape and anti-tumor immunity has remained unclear. Through integrated analysis of ITH and neoantigen burden, we demonstrate the impact of clonal neoantigens, present in every cancer cell, on survival in primary lung adenocarcinoma. We identify neoantigen-reactive CD8+ T cells recognizing clonal neoantigens in patients with early stage NSCLC and demonstrate expression of high levels of co-inhibitory immune checkpoint molecules including PD-1. In keeping with these observations, sensitivity to CTLA-4 and PD-1 blockade in patients with advanced melanoma and NSCLC was enhanced in tumors enriched for clonal neoantigens.
Heterogeneity in the neoantigen landscape may therefore influence immune surveillance. Clonal neoantigens, shared by all tumor cells, represent a key substrate for T cell recognition and an attractive target for adoptive cell-based and vaccination strategies which may hold promise to address the challenges of ITH.
Citation Format: Andrew J. S. Furness. Novel insights into T cell recognition and regulation at the tumor site. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Targeting the Vulnerabilities of Cancer; May 16-19, 2016; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(1_Suppl):Abstract nr IA19.
Traditional Cardiovascular Risk Factors and Their Relation to Future Surgery for Valvular Heart Disease or Ascending Aortic Disease: A Case–Referent Study
Authors: Ljungberg Johan , Johansson Bengt , Engström Karl Gunnar , Albertsson Elin , Holmer Paul , Norberg Margareta , Bergdahl Ingvar A. , Söderberg Stefan 
Published: May 2017

Background
Risk factors for developing heart valve and ascending aortic disease are based mainly on retrospective data. To elucidate these factors in a prospective manner, we have performed a nested case–referent study using data from large, population‐based surveys.

Methods and Results
A total of 777 patients operated for heart valve disease or disease of the ascending aorta had previously participated in population‐based health surveys in Northern Sweden. Median time (interquartile range) from survey to surgery was 10.5 (9.0) years. Primary indications for surgery were aortic stenosis (41%), aortic regurgitation (12%), mitral regurgitation (23%), and dilatation/dissection of the ascending aorta (17%). For each case, referents were allocated, matched for age, sex, and geographical area. In multivariable models, surgery for aortic stenosis was predicted by hypertension, high cholesterol levels, diabetes mellitus, and active smoking. Surgery for aortic regurgitation was associated with a low cholesterol level, whereas a high cholesterol level predicted surgery for mitral regurgitation. Hypertension, blood pressure, and previous smoking predicted surgery for disease of the ascending aorta whereas diabetes mellitus was associated with reduced risk. After exclusion of cases with coronary atherosclerosis, only the inverse associations between cholesterol and aortic regurgitation and between diabetes mellitus and disease of the ascending aorta remained.

Conclusions
This is the first truly prospective study of traditional cardiovascular risk factors and their association with valvular heart disease and disease of the ascending aorta. We confirm the strong association between traditional risk factors and aortic stenosis, but only in patients with concomitant coronary artery disease. In isolated valvular heart disease, the impact of traditional risk factors is varying.