bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract LB-96: A novel blood preservation system to study oncogenic signaling pathway biomarkers by flow cytometry in leukemia/lymphoma clinical trials
Authors: Pahuja Anil , Saci Abdel , Sarikonda Shyam , Graber Armin , Lee Benjamin , Lameh Jelveh , Tangri Shabnam , Dakappagari Naveen
Published: May 2015

Propelled by the advent of new technologies and an evolving regulatory landscape, the desire to personalize cancer treatments has never been greater. There is a critical need to reliably evaluate target inhibition and pharmacodynamic activity of investigational drugs in biologically relevant compartments. However, the ability to fulfill such a task in global clinical trials is complicated by varying technical expertise available at clinical sites and considerations about specimen stability for centralized laboratory analysis. We developed a novel formalin-based preservation method that enables specimen stabilization in a single step, requiring less than 20 minutes, without the need for specialized training or instrumentation. Stabilized specimens can be frozen for shipping and batched analysis at a later time point, in a specialized laboratory. Using this preservation method, we developed a flow assay enabling identification of multiple cell-types, and quantification of intracellular biomarkers in target cellular compartments, in both the peripheral blood (PB) and bone marrow (BM). We present pharmacodynamic (PD) data for a novel anticancer investigational agent intended for acute myeloid leukemia and multiple myeloma and its effect on multiple target biomarkers of the PI3K signaling pathway, including phosphorylation of the S6 ribosomal protein (S6). Our novel fixation method allowed detection of pS6 modulation in a dose dependent manner in both tumor cells and PB or BM in response to the novel investigational agent. Assay sensitivity and concordance were evaluated by comparing flow assay with western blot analysis, with each assay performed at a different site using the same batched frozen samples; exceptional preservation of phosphorylated proteins for more than 72 hours could be observed, when frozen immediately following fixation. In conclusion, our novel preservation method enables reliable quantification of signaling biomarkers in centralized laboratories at different time points post sample (PB or BM) acquisition requiring minimal processing at collection sites.

Citation Format: Anil Pahuja, Abdel Saci, Shyam Sarikonda, Armin Graber, Benjamin Lee, Jelveh Lameh, Shabnam Tangri, Naveen Dakappagari. A novel blood preservation system to study oncogenic signaling pathway biomarkers by flow cytometry in leukemia/lymphoma clinical trials. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-96. doi:10.1158/1538-7445.AM2014-LB-96
Abstract LB-99: Identification and characterization of small molecule thieno[3,2-d]pyrimidine inhibitors of Protein Kinase C iota (PKCι)
Authors: Soudy Christelle , Stanway Emma , Patel Bhavisha , Barton Caroline , Barnard Michelle , Pang Leon , Owen Paul , Turnbull Andrew , Ruggeri Bruce A. , Dorsey Bruce D. , Ator Mark A. , Ott Greg R. , Linch Mark , Riou Philippe , Parker Peter J. , Kjaer Sven , Dillon Christian , McDonald Neil Q. , Roffey Jon
Published: May 2015

We describe a novel series of small molecule ATP-competitive inhibitors of the atypical class of Protein Kinase C (PKC). The PKC family of serine/threonine kinases are divided into four structurally and functionally distinct sub-types: classic (PKCα, PKCβ, PKCγ); novel (PKCδ, PKCε, PKCη, PKCθ); atypical (PKCι,PKCζ); and PKNs (PKN1, PKN2, PKN3). The PKCs have been defined as key regulators in a multitude of signal transduction pathways that impinge on diverse cellular processes such as proliferation, differentiation, and survival. The regulation and functions of the atypical PKCs are distinct from the classic and novel PKCs.Both atypical isoforms have been implicated in various models of cancer, and PKCι in particular has been described as a potential oncogene. Its abundance is frequently increased, primarily through PKCι gene amplification, in many epithelial tumours including: subsets of squamous non-small cell lung carcinoma, serous ovarian carcinoma, and squamous esophageal carcinoma. It has been widely demonstrated that deregulation of PKCι signalling leads to unconstrained cell growth, increased migratory and invasive behaviour, and aberrant cellular polarity, which is a hallmark of aggressive cancers. Together, these data make a strong case for the inhibition of PKCι as a novel therapeutic strategy. We have discovered a series of ATP-competitive thieno[3,2-d]pyrimidine- based PKCι inhibitors from a high throughput screen. Using structure-based design we have optimized the series and demonstrated potent and selective inhibition of PKCι in biochemical and cellular models. The biochemical, structural, and cellular characterization of these compounds will be described herein.

Citation Format: Christelle Soudy, Emma Stanway, Bhavisha Patel, Caroline Barton, Michelle Barnard, Leon Pang, Paul Owen, Andrew Turnbull, Bruce A. Ruggeri, Bruce D. Dorsey, Mark A. Ator, Greg R. Ott, Mark Linch, Philippe Riou, Peter J. Parker, Sven Kjaer, Christian Dillon, Neil Q. McDonald, Jon Roffey. Identification and characterization of small molecule thieno[3,2-d]pyrimidine inhibitors of Protein Kinase C iota (PKCι). [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-99. doi:10.1158/1538-7445.AM2014-LB-99
Abstract SY05-02: Targeting kinases with reversible covalent fragments
Authors: Taunton Jack
Published: May 2015

The clinical utility of targeting kinases with covalent drugs has been firmly established, culminating in the recent FDA approval of afatinib and ibrutinib, which irreversibly inhibit the tyrosine kinases, EGFR and BTK. More broadly, chemical probes that form a covalent bond with a nonconserved, noncatalytic cysteine often show enhanced potency, selectivity, and utility in biological studies. Despite these advantages, protein-reactive compounds are usually avoided in high-throughput screening campaigns. Motivated by a desire to explore the chemistry of reactive electrophiles and thiols under physiological conditions, we initiated a study of Michael acceptors bearing substituents with increasing electron withdrawing capacity. We hypothesized that the intrinsically labile nature of the cysteine/cyanoacrylamide bond could be exploited to yield cysteine-targeted, reversible covalent inhibitors. These concepts led to the design of ultra-selective cyanoacrylamide-based RSK inhibitors with picomolar affinity and slow dissociation kinetics, the structural basis of which was revealed by x-ray crystallography. The intrinsically reversible, yet thermodynamically favorable nature of the cysteine/cyanoacrylamide bond suggested that this ‘sweet spot’ in electrophile space could form the basis of a fragment-based approach to ligand discovery. Screening a collection of cyanoacrylamide fragments against three kinases (RSK2, NEK2, and PLK1) containing a structurally equivalent cysteine delivered unique inhibitors for all three kinases with potencies in the submicromolar range. Optimization guided by x-ray crystallography rapidly led to the first dual inhibitor of MSK and RSK, with subnanomolar affinity and >500-fold selectivity over NEK2 and PLK1. In close collaboration with Brian Shoichet and Nir London, we have employed covalent docking methods to screen large virtual libraries of electrophilic fragments. We designed a pilot virtual library of 13,000 cyanoacrylamide fragments that can be synthesized in one simple step from commercially available aldehydes. A virtual screen of this library rapidly led to novel inhibitors of NEK2, PLK-, and MSK/RSK-family kinases. Finally, I will discuss our efforts to discover and design new electrophilic chemotypes that form reversible covalent bonds with cysteine residues.

Citation Format: Jack Taunton. Targeting kinases with reversible covalent fragments. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY05-02. doi:10.1158/1538-7445.AM2014-SY05-02
Abstract SY05-03: Natural product-inspired peptide drug discovery accelerated by the RaPID system
Authors: Suga Hiroaki
Published: May 2015

Despite the fact that natural products are attractive resources for the discovery of drug candidates, the screening processes often not only time-consuming and labor-intensive but also high risk to obtain potent molecules. We have previously devised a new means to reprogram the genetic code, which allows us to express macrocyclic peptides using a custom-made in-vitro translation system. Its integration with the mRNA display technique has also led to the development of a means of selecting bioactive macrocyclic peptides, referred to as RaPID (Random non-standard Peptide Integrated Discovery) system. This lecture will describe some of recent examples for the discovery of such natural product-inspired macrocycles and pseudo-natural products with their therapeutic applications.

Citation Format: Hiroaki Suga. Natural product-inspired peptide drug discovery accelerated by the RaPID system. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY05-03. doi:10.1158/1538-7445.AM2014-SY05-03
Abstract SY05-04: Biological discovery and therapeutic insight from DNA-templated macrocycle libraries
Authors: Liu David R.
Published: May 2015

DNA-templated organic synthesis enables the translation of libraries of DNA templates into corresponding libraries of synthetic small molecules. The in vitro selection of a library of DNA-templated small-molecule macrocycles has resulted in the discovery of unusually selective and potent inhibitors of kinase, protease, and protein-protein interface targets. Using this approach, we recently discovered the first physiologically active inhibitor of an enzyme implicated in type-2 diabetes. In a series of biochemical, structural biological, and in vivo physiology experiments, we elucidated the molecular basis of target inhibition by this macrocycle, validated a new target for the potential treatment of type-2 diabetes, and discovered previously unknown and therapeutically relevant physiological roles for this enzyme.

Citation Format: David R. Liu. Biological discovery and therapeutic insight from DNA-templated macrocycle libraries. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY05-04. doi:10.1158/1538-7445.AM2014-SY05-04
Abstract SY06-02: Revisiting the STATs of cancer: Emergence of stem-like cancer cells
Authors: Jove Richard
Published: May 2015

Activation of the STAT3 signaling pathway is now well established as an important factor in cancer progression and as a promising molecular target for cancer therapy. Persistent STAT3 activation in tumor cells prevents apoptosis and promotes cell proliferation. In the tumor microenvironment, STAT3 activation enhances angiogenesis and suppresses anti-tumor immune responses. Communication between tumor cells and stromal cells in the tumor microenvironment, by inflammatory cytokines like interleukin (IL)-6, results in a feed-forward loop that enhances cancer progression and confers resistance to therapy. Recently, we have uncovered another critical role for STAT3 in cancer progression and resistance to therapy. We now show that activation of STAT3 signaling promotes a stem-like cell phenotype in prostate cancer, concomitant with loss of androgen receptor (AR) expression. AR is important for prostate cancer progression, and androgen deprivation often leads to drug resistance and eventual cancer recurrence. We demonstrate that loss of AR expression as a consequence of androgen ablation results in STAT3 activation in prostate cancer cells. This STAT3 activation in turn leads to development of prostate cancer stem-like cells. AR downregulation-induced STAT3 activation is mediated through increased IL-6 expression in the tumor microenvironment. Elevated stem-like cell markers in human prostate tumor specimens coincides with high STAT3 activity and low AR expression. Treatment of mice with soluble IL-6 receptor or silencing STAT3 in tumor cells suppresses prostate tumor growth and inhibits development of stem-like cancer cells. In sum, our results demonstrate that blockade of AR mediates activation of STAT3 signaling through up-regulation of IL-6, which is associated with development of a stem-like cancer cell phenotype. Conversely, inhibition of the IL-6/STAT3 pathway diminishes the stem-like cancer cell population, and results in reduced tumor growth. Our findings provide new mechanistic insights into the role of STAT3 activation upon AR blockade on prostate cancer relapse and drug resistance. We further propose inhibition of STAT3 signaling in combination with anti-androgens as a potential strategy to prevent emergence of drug-resistant recurrent prostate cancer.

Citation Format: Richard Jove. Revisiting the STATs of cancer: Emergence of stem-like cancer cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY06-02. doi:10.1158/1538-7445.AM2014-SY06-02
Abstract SY13-04: Stem cell self-renewal and cancer
Authors: Morrison Sean J.
Published: May 2015

Haematopoietic stem cell self-renewal and leukemogenesis

“Pre-leukemic” mutations are thought to promote clonal expansion of haematopoietic stem cells (HSCs) by increasing self-renewal and competitiveness; however, mutations that increase HSC proliferation tend to reduce competitiveness and self-renewal potential, raising the question of how a mutant HSC can sustainably outcompete wild-type HSCs. Activating mutations in NRAS are prevalent in human myeloproliferative neoplasms and leukemia. We found that a single allele of oncogenic NrasG12D increases HSC proliferation but also increases reconstituting and self-renewal potential upon serial transplantation in irradiated mice, all prior to leukemia initiation. NrasG12D also confers long-term self-renewal potential upon multipotent progenitors. To explore the mechanism by which NrasG12D promotes HSC proliferation and self-renewal we assessed cell cycle kinetics using H2B-GFP label retention and BrdU incorporation. NrasG12D had a bimodal effect on HSCs, increasing the rate at which some HSCs divide and reducing the rate at which others divide. This mirrored bimodal effects on reconstituting potential as rarely dividing NrasG12D HSCs outcompeted wild-type HSCs while frequently dividing NrasG12D HSCs did not. NrasG12D had these effects by promoting STAT5 signaling, inducing different transcriptional responses in different subsets of HSCs. One signal can therefore increase HSC proliferation, competitiveness, and self-renewal through bimodal effects on HSC gene expression, cycling, and reconstituting potential.

We have also developed methods for studying protein synthesis by individual stem cells in vivo. Currently, there are almost no data on protein synthesis in any somatic stem cell. We found that the amount of protein synthesized per hour in HSCs in vivo was lower than in most other haematopoietic cells, even if we controlled for differences in cell cycle status or forced HSCs to undergo self-renewing divisions. Reduced ribosomal function in Rpl24Bst/+ mice further reduced protein synthesis in HSCs and impaired HSC function. Pten deletion increased protein synthesis in HSCs but also reduced HSC function. Rpl24Bst/+ cell-autonomously rescued the effects of Pten deletion in HSCs, blocking the increase in protein synthesis, restoring HSC function, and delaying leukemogenesis. Pten deficiency thus depletes HSCs and promotes leukemia partly by increasing protein synthesis. Increased or decreased protein synthesis impairs HSC function.

Citation Format: Sean J. Morrison. Stem cell self-renewal and cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY13-04. doi:10.1158/1538-7445.AM2014-SY13-04
Abstract SY20-03: Nuclear-mitochondrial cross-talk: A key determinant of cancer metastasis
Authors: Welch Danny R. , Liu Wen , Feeley Kyle P. , Ballinger Scott W.
Published: May 2015

Despite the well known energy requirements and stresses of metastasis, the relationships between metabolism, mitochondrial genetics and metastasis are still underdeveloped. Two lines of investigation point to more intimate involvement of mtDNA than is widely appreciated. First, recent data demonstrate that the metastasis suppressor KISS1 essentially reverses the so-called Warburg Effect by regulating mitochondrial biogenesis. KISS1 re-expression results in higher pH[Ex] due to reduced lactate secretion concomitant with reduced glycolysis and a shift toward oxidative phosphorylation. KISS1-expressing cells have 30-50% more mitochondrial mass, which appears to be due to higher expression of PPARγ co-activator 1α (PGC1α), a master regulator of mitochondrial biogenesis. shRNA-mediated knockdown of KISS1 and PGC1α establish a pathway between these molecules, mitochondrial biogenesis and metastatic potential. Second, genetic crosses with a newly described MNX (mitochondrial-nuclear exchange) mice suggest that mitochondrial polymorphisms (haplotypes) may control susceptibility to metastasis. Transgenic FVB/N-tg:MMTV-PyMT which spontaneously develop mammary tumors and lung metastasis with high penetrance were crossed with female MNX mice having the same nuclear background (FVB - wild-type) but with C57BL/6 and BALB/c mitochondrial backgrounds. Using this strategy, the mtDNA contributions to metastasis can be discriminated. Results demonstrate that tumor and metastasis incidence do not appear to be significantly different. However, metastasis size is greatly affected. Taken together, these data strongly support the concept that mitochondrial-nuclear cross-talk is a more significant determinant of metastasis than generally appreciated. SUPPORT: NCI-CA134981; Natl Fndn Cancer Res, Susan G. Komen SAC11037, Hall Family Fndn, KS Bioscience Auth.

Citation Format: Danny R. Welch, Wen Liu, Kyle P. Feeley, Scott W. Ballinger. Nuclear-mitochondrial cross-talk: A key determinant of cancer metastasis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY20-03. doi:10.1158/1538-7445.AM2014-SY20-03
Abstract SY28-03: Whole genome pictures of live cancers and personalized medicine
Authors: Nakagawa Hidewaki
Published: May 2015

Primary liver cancer is one of the most common and deadly cancers worldwide, especially in Asia, and has no effective treatment, yet its molecular mechanism remains largely unknown. Although virus-related HCC is a major form of primary liver cancer in Asia, their etiology and phenotype are very heterogeneous (HBV-infected, HCV-infected, or non-viral, and HCC or biliary phenotype). To explore whole genomic alterations and diversity of liver cancers, we performed whole genome sequencing (WGS) analysis integrated with RNA-seq on ∼270 liver cancers, demonstrating comprehensive landscape of diverse phenotypes of liver cancers with multiple etiological backgrounds for point mutations, short indels, copy-number alterations, structural variations, and HBV integrations. On average, approximately 10,000 somatic alterations per one tumor were identified by WGS, and our study indicated the genomic heterogeneity of liver cancer genomes as well as their etiological heterogeneity and that somatic substitution patterns of cancer genomes could be determined by their etiological backgrounds such as carcinogen exposure and cell origins. Understanding of liver cancer genome heterogeneity underlying its biological phenotype and interpreting its genomic data could facilitate cancer biomarkers discovery and personalized medicine, where we can select old and new drugs to each of cancer patients by using their diverse genome information.

Citation Format: Hidewaki Nakagawa. Whole genome pictures of live cancers and personalized medicine. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY28-03. doi:10.1158/1538-7445.AM2014-SY28-03
Abstract SY29-04: Beyond necroptosis - regulated necrosis in the kidney
Authors: Linkermann Andreas
Published: May 2015

Regulated necrosis (RN) may result from cyclophilin D (CypD)-mediated mitochondrial permeability transition (MPT) and receptor-interacting protein kinase 1 (RIPK1)- mediated necroptosis, ferroptosis, pyroptosis, NADPH-oxidase (NOX) mediated necrosis and other pathways, but it is currently unclear to what extent these signaling pathways are independent from each other. Especially MPT and necroptosis have been described to contribute to necrotic cell death in kidney ischemia reperfusion injury (IRI). We demonstrate that necroptosis in IRI occurs in mice as primary organ damage, independent of the immune system, and that mice deficient for RIPK3, the essential downstream partner of RIPK1 in necroptosis, are protected from IRI and the level of protection was significantly stronger than of CypD-deficient mice. Several lines of evidence in vitro and in vivo, including the analysis of cisplatin-induced acute kidney injury and hyperacute TNF-shock models in mice suggested the distinctness of CypD-mediated MPT from RIPK1/RIPK3-mediated necroptosis. In addition, we found necroptosis to be completely independent of mitochondria in vitro and therefore generated CypD-RIPK3 double-deficient mice that are viable and fertile without an overt phenotype and that survived prolonged IRI which was lethal to each single knockout. Combined application of the RIPK1 inhibitor necrostatin-1 (Nec-1) and the MPT inhibitor sanglifehrin A (SfA) confirmed the results with mutant mice. The data demonstrate the pathophysiological co-existence and co-relevance of two separate pathways of RN in IRI and suggest that combination therapy targeting distinct RN pathways can be beneficial in the treatment of ischemic injury.

Citation Format: Andreas Linkermann. Beyond necroptosis - regulated necrosis in the kidney. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY29-04. doi:10.1158/1538-7445.AM2014-SY29-04
Abstract SY31-02: Building highly effective anti-tumor T cells
Authors: Restifo Nicholas P.
Published: May 2015

Many tumors contain relatively undifferentiated transformed progenitors termed ‘cancer stem cells’ (CSC). Stem cells are defined by the ability to self-renew and generate differentiated progeny, qualities maintained by evolutionarily conserved pathways that can lead to cancer when deregulated. The existence of stem cells has been documented across multiple tissues both during development on into adulthood including the hematopoietic and central nervous systems, intestine, skin, cardiac muscle and lung. All of these sites employ the presence of limited numbers of stem cells in tissues enable a few daughter cells to retain a regenerative potential while the majority of daughter cells enter an irreversible process of differentiation culminating in the generation of specialized cell types. Recently, we have found evidence supporting the existence and function of stem cells within the adaptive immune system in both the CD8+ and CD4+ T cell lineages. This stem cell-like population has been termed ‘T memory stem cells’ (TSCM). In preclinical models using both mouse and human cells, TSCM can overcome many limitations of currently employed T cell-based immunotherapies, especially in the setting of adoptive T cell transfer, including inefficient T cell engraftment, persistence, and ability to mediate prolonged immune attack. Conferring stemness to anti-tumour T cells might unleash the full potential of cellular therapies. Our goal is to trigger stem cell-like pathways in tumor-reactive T cells or to reprogram terminally differentiated tumor-infiltrating lymphocytes (TILs) to confer stem cell-like properties to augment immunotherapies against cancer and CSC, akin to fighting ‘fire with fire.’ In new work from our laboratory (1) as well as unpublished experiments, we have identified several candidate transcription factors that are differentially expressed in stem cell-like T cells. In addition, new experiments have shed significant light on the metabolic properties of highly effective stem cell-like T cell subsets.

Reference

1. Roychoudhuri, R, et al, Nature, 2013.

Citation Format: Nicholas P. Restifo. Building highly effective anti-tumor T cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY31-02. doi:10.1158/1538-7445.AM2014-SY31-02
Abstract SY32-04: Defects in T cell migration within tumors: a role for extracellular matrix architecture
Authors: Donnadieu Emmanuel
Published: May 2015

T cell-based immunotherapies have given promising results in patients with metastatic melanoma. However, a significant proportion of cancer patients did not respond to these therapeutic interventions for reasons that are not understood. To attack a tumor, T cells need to be correctly primed in the tumor-draining lymph nodes, enter into the tumor, navigate within the tumor environment and then mediate their effector functions to cause destruction of cancer cells. All of these criteria that rely on proper migration of T cells must be met for a treatment to be effective. By using fluorescence imaging techniques, we have made significant progress in the understanding of how T cells are blocked in their migratory activities and have identified several obstacles. The first occurs in tumor-draining lymph nodes as our data reveal the existence of marked cellular and structural changes that limit T cells from migrating and performing their surveillance activity. Another alteration concerns the poor ability of T cells to contact malignant cells within tumors. Indeed, in several human carcinomas, T cells are far from malignant cells but enriched in the stroma composed of non-tumors cells along with the extracellular matrix. We have identified the matrix structure as an important stromal component in controlling the ability of T cell to migrate and mount antitumor immune response. Whereas reticular fiber networks favor T cell navigation, dense and aligned matrix fibers act as unfavorable migration zones for T cells. Such fibrotic structures, which are frequently observed around tumor islets, contribute to the poor capacity of T cells to contact and kill tumor cells.

Thus, abnormal extracellular matrix, as observed in solid tumors, can be considered another important player of the tumor stroma involved in blocking T cells in their antitumor activities. A new challenge in cancer therapy will be to develop approaches aimed at altering the architecture of the tumor stroma rendering it more permissive to antitumor T cells.

Citation Format: Emmanuel Donnadieu. Defects in T cell migration within tumors: a role for extracellular matrix architecture. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY32-04. doi:10.1158/1538-7445.AM2014-SY32-04
Abstract SY36-01: Functional genomics and cancer dependencies
Authors: Hahn William C.
Published: May 2015

Recent advances in genomics continue to elucidate the genetic lesions that occur in specific cancers and are increasingly being applied prospectively to patient samples in the clinic. These efforts have already identified a large number of mutations that occur at low frequency. Systematic approaches to identify cancer vulnerabilities will provide critical information about the function of these low frequency mutations and will allow the identification of cancer co-dependencies and synthetic lethal interactions. Over the past several years, we have developed genome scale RNAi libraries and open reading frame expression libraries that permit a systematic evaluation of genes involved in cancer initiation and maintenance. Using these libraries, we have now performed screens in a large panel of human cancer cell lines to systematically identify cancer vulnerabilities. By combining these functional approaches with information derived from mapping the structural abnormalities present in cancer genomes, we have identified several new oncogenes that contribute to cancer development as well as co-dependencies that are required for the survival of cancers harboring specific mutations. The ability to systematically manipulate gene expression at genome scale now provides opportunities to investigate the function of genes involved in cancer initiation and maintenance, which will provide a framework for therapeutic strategies.

Citation Format: William C. Hahn. Functional genomics and cancer dependencies. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY36-01. doi:10.1158/1538-7445.AM2014-SY36-01
Abstract SY36-03: How aneuploidy drives tumorigenesis
Authors: Davoli Teresa , Xu Wei , Park Peter , Elledge Stephen J.
Published: May 2015

Aneuploidy has been recognized as a hallmark of cancer for over 100 years, yet no general theory to explain the recurring patterns of aneuploidy in cancer has emerged. Here we describe the development of Tumor Suppressor and Oncogene (TUSON) Explorer, a computational method that analyzes the patterns of mutational signatures in tumors and predicts the likelihood that any individual gene functions as a tumor suppressor (TSG) or oncogene (OG). By analyzing >8200 tumor-normal pairs we provide statistical evidence suggesting many more genes possess cancer driver properties than anticipated, forming a continuum of oncogenic potential. Integrating our driver predictions with information on somatic copy number alterations, we find that the distribution and the potency of TSGs (STOP genes), OGs and essential genes (GO genes) on chromosomes can predict the complex patterns of aneuploidy and copy number variation characteristic of cancer genomes. We propose that the cancer genome is shaped through a process of cumulative haploinsufficiency and triplosensitivity.

Citation Format: Teresa Davoli, Wei Xu, Peter Park, Stephen J. Elledge. How aneuploidy drives tumorigenesis. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY36-03. doi:10.1158/1538-7445.AM2014-SY36-03
Abstract SY42-02: Sensitization to chemoradiation by inhibition of cell cycle checkpoints
Authors: Morgan Meredith Ann
Published: May 2015

Chemoradiation is uniquely effective at generating DNA DSBs (double-strand breaks) in the environment of chemotherapy-induced DNA damage and replication stress producing complex, difficult-to-repair DNA DSBs. However, chemoradiation therapy also initiates robust cell cycle checkpoint responses in tumor cells which promote repair of DNA damage and thus contribute to therapy resistance. Thus, inhibition of cell cycle checkpoints by inhibitors of kinases such as Wee1 or Chk1 is an especially effective strategy for sensitizing tumor cells to chemoradiation. In addition to abrogating cell cycle checkpoints, inhibitors of Wee1 and Chk1 inhibit homologous recombination repair of DNA DSBs. Furthermore, the efficacy of PARP1/2 [poly (ADP- ribose) polymerase1/2] inhibitors in homologous recombination repair defective tumor cells provides a rationale for the combination of Wee1 or Chk1 inhibitors with PARP1/2 inhibitors and radiation. Clinical investigation of Wee1 inhibitors with chemoradiation has recently been initiated. Novel combinations of targeted agents such as Wee1 and PARP1/2 inhibitors with radiation are an important area of emphasis for future clinical studies. Preclinical studies to define optimal agent combinations and scheduling, mechanisms of tumor cell selectivity, and biomarkers will improve the likelihood of clinical success for these combinations.

Citation Format: Meredith Ann Morgan. Sensitization to chemoradiation by inhibition of cell cycle checkpoints. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY42-02. doi:10.1158/1538-7445.AM2014-SY42-02
Abstract SY44-02: Insights into pro-survival signaling by PERK
Authors: Diehl J. Alan
Published: May 2015

PERK, one of three key signal transducers localized to the Endoplasmic Reticulum (ER), regulates cell fate in response to proteotoxic stress. PERK activation can be triggered by exposure of cells to physiological stresses such as low energy (glucose deprivation), low oxygen (hypoxia), or by chemical that inhibit protein degradation (bortezomib) or deplete ER calcium stores (thapsigargin). Since tumor survival and progression requires bypass of many of the same stresses that are known to activate PERK, extensive efforts have been undertaken to ascertain whether targeted inhibition of PERK would have therapeutic benefit. Indeed, genetic abrogation of PERK signaling has a profound influence on tumor progression and metastasis supporting the development of small molecule PERK inhibitors. Importantly, the successful use of such small molecules in a clinical setting requires knowledge of both the potential tissue toxicities associated with acute PERK inhibition and a detailed understanding of downstream PERK effectors that contribute to cell growth and survival. To definitively establish the functional role of PERK in the adult tissue, we have generated mice harboring a conditional PERK allele where excision is regulated by tamoxifen administration. In contrast to previous reports, PERK deletion has a profound impact on pancreata regardless of age. This result has profound implications for the utility of small molecule PERK inhibitors and highlights the need to clearly delineate downstream PERK-dependent regulatory pathways. With this in mind, we have set out to define additional pro-survival PERK effector and effector pathways in an effort to develop a more complete understanding of PERK function and ascertain whether any novel effectors might represent opportunities for therapeutic development. The identification and contribution of novel PERK effectors will be discussed.

Citation Format: J. Alan Diehl. Insights into pro-survival signaling by PERK. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY44-02. doi:10.1158/1538-7445.AM2014-SY44-02
Abstract 10: DNA repair and nutritional risk models of triple-negative breast cancer
Authors: Hu Jennifer , Lee Eunkyung , Allen Glenn
Published: May 2015

Purpose: Triple negative breast cancer (TNBC), which lacks treatment targets for estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2), has been associated with African-American race, BRCA1/2 mutations, TP53 mutations, and poor prognosis. However, the etiology of TNBC remained unknown, which represents a critical barrier in reducing breast cancer mortality. Therefore, we designed a case-only study to test combined genetic and nutritional risk models of TNBC.

Methods: In 354 breast cancer patients diagnosed between 1998 and 2004, we evaluated 18 DNA-repair non-synonymous single nucleotide polymorphisms (nsSNPs) using the Sequenom MassARRAY system. The 110-item Block 1998 food frequency questionnaire was used to evaluate dietary/nutritional intakes. The Multivariate Adaptive Regression Splines (MARS)-logit models were used to define nutritional intakes cut-offs for their associations with TNBC.

Results: TNBC was associated with 6 DNA-repair nsSNPs, ERCC4 R415Q (rs1800067), MSH3 R940Q (rs184967), MSH6 G39E (rs1042821), POLD1 R119H (rs1726801), XRCC1 R194W (rs1799782), and XPC A499V (rs2228000) and/or 3 micronutrients (zinc, folate, and β-carotene). Combined DNA-repair risk genotypes and lower micronutrient intakes had a significant dosage-dependent association with TNBC (p<0.001): ORs=2.77 (95%CI=1.01-7.64), 9.57 (95%CI=2.87-31.84), and 20.78 (95%CI=2.46-175.71) for 2, 3, and at least 4 risk factors combined, respectively.

Conclusion: To the best of our knowledge, this is the first study to demonstrate multiple DNA repair nsSNPs and nutritional factors are associated with TNBC. Our results suggest that dietary modulation and micronutrient supplementation may have implication in preventing or reversing TNBC, particularly in genetically susceptible women.

Citation Format: Jennifer Hu, Eunkyung Lee, Glenn Allen. DNA repair and nutritional risk models of triple-negative breast cancer. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Susceptibility and Cancer Susceptibility Syndromes; Jan 29-Feb 1, 2014; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(23 Suppl):Abstract nr 10. doi:10.1158/1538-7445.CANSUSC14-10
Abstract 21: Quantitative FRET technology for SUMOylation cascade and high-throughput screening assay for SUMOylation inhibitor in cancer drug discovery
Authors: Liao Jiayu , Wiryawan Hilda , Li Yang , Song Yang , Liu Yan , You Jiacong , Jiang Ling , Malik Harbani Kaur , Saavedra Amanda N. , Qu Sophie
Published: May 2015

The ubiquitin–proteasome system and ubiquitin-like protein pathways, such as SUMOylation, are critical in protein homeostasis and activities in vivo and are emerging as a new strategy to treat many acute and chronic human diseases, such as cancers. Although various kinase inhibitors have been developed as target-based therapy, solid tumors are still challenges in clinical therapy because various resistant are developed after kinase inhibitor treatments, and therapeutic agents with novel mechanisms are urgently needed. SUMO has been shown to modify various critical proteins, such as p53, MDM2, Estrogen receptor and androgen receptors. More recently, a genome-wide siRNA screening shown that inhibition of SUMO E1 ligases can lead to synergistically lethality of c-Myc overexpressed breast cancer cells. However, so far, specific inhibitor of SUMOylation is still not available for the community.

Fig. 1. SUMOylation in human diseases and quantitative systems biology approach for basic and translational research of SUMOylation. We developed a novel quantitative Förster resonance energy transfer (FRET) technology platform for both basic kinetics parameter determinations and high-through screening(HTS) assays for SUMOylation cascade. The novel theoretical and experimental procedures for protein interactions affinity(Kd) determinations in the SUMOylation cascade, including the interaction between SUMO1 and its E2 ligase, Ubc9, E1 heterodimers(Aos1 and Uba2), E1 and E2 interactions(Uba2 and Ubc9), and E2 and substrate interactions(Ubc9 and RanGap1c) and protease kinetics, Kcat/KM of SENP1 endopeptidase activity have been developed in a systems biology manner. The data are in good agreement with traditional methods. Multiple FRET-based HTS assays have also been developed and HTS campaigns have led to very promising hit that can preferentially kill Non-small cell lung cancer cells. The novel SUMOylation inhibitor can be used for cancer treatments by synergistically lethality strategy.

Citation Format: Jiayu Liao, Hilda Wiryawan, Yang Li, Yang Song, Yan Liu, Jiacong You, Ling Jiang, Harbani Kaur Malik, Amanda N. Saavedra, Sophie Qu. Quantitative FRET technology for SUMOylation cascade and high-throughput screening assay for SUMOylation inhibitor in cancer drug discovery. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Susceptibility and Cancer Susceptibility Syndromes; Jan 29-Feb 1, 2014; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(23 Suppl):Abstract nr 21. doi:10.1158/1538-7445.CANSUSC14-21
Abstract 28: Chemoprevention strategies to target abnormal imprinting in high-risk African American women who do or do not carry a BRCA1 mutation
Authors: Seewaldt Victoria , Skaar David , Dietze Eric , Desai Shraddha , Jirtle Randy
Published: May 2015

Background: Genomic imprinting is an inherited form of parent-of-origin-specific epigenetic gene regulation that is dysregulated by poor prenatal nutrition and environmental toxins. KCNK9 encodes TASK3, a pH-regulated potassium channel membrane protein that is overexpressed in 40% of breast cancer. KCNK9 gene amplification accounts for increased expression in <10% of these breast cancers.

Methods/Results: Here we show that KCNK9 has imprinted expression in breast tissue and provide the first identification of the KCNK9 DMR and DMR-associated open chromatin. Our studies show that loss of KCNK9 regulatory methylation and imprinted expression occurs in 75% of triple-negative breast cancer (TNBC) and loss of methylation occurs in non-cancerous tissue from high-risk women. Functional studies show that TASK3 protein regulates mitochondrial membrane potential and apoptosis-sensitivity. In live TNBC cells and non-cancerous mammary epithelial cells from high-risk women, loss of KCNK9 DMR methylation predicts increased mitochondrial membrane potential (p=0.007). African American women have a significantly higher frequency of loss of KCNK9 imprinting than do risk-matched Caucasian women (p=0.005). African American women with BRCA1 mutation have the highest frequency of loss (p<0.0001).

Clinical Prevention: This is the first identification of the KCNK9 DMR and demonstration that loss of methylation and overexpression of TASK3 increases mitochondrial membrane potential and promotes apoptosis resistance. Low-toxicity inhibitors of TASK3 are in clinical use and can be readily re-purposed to provide cost effective chemoprevention. These inhibitors include K+ inhibitors (developed for cardiac indications) and Schwann Pepper. Our studies identify TASK3 as a “drugable”, low-toxicity target that can be readily employed as a novel target for prevention and treatment of TNBC, particularly in high-risk African American women.

Citation Format: Victoria Seewaldt, David Skaar, Eric Dietze, Shraddha Desai, Randy Jirtle. Chemoprevention strategies to target abnormal imprinting in high-risk African American women who do or do not carry a BRCA1 mutation. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Susceptibility and Cancer Susceptibility Syndromes; Jan 29-Feb 1, 2014; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(23 Suppl):Abstract nr 28. doi:10.1158/1538-7445.CANSUSC14-28
Abstract 33: Interplay of DNA damage and cell cycle signaling on Replication Protein A in human cells
Authors: Brader Kerry , Mosel Adam , Liu Shengqin , Kremmer Elizabeth , Goettsch Kaitlin , Nasheuer Heinz-Peter , Oakley Greg , Borgstahl Gloria
Published: May 2015

Replication protein A (RPA) is the main human single-stranded DNA (ssDNA)-binding protein. It is essential for cellular DNA metabolism and has important functions in DNA damage signaling. RPA is indispensable for accurate homologous recombination (HR)-based DNA double-stranded break (DSB) repair and its activity is regulated by phosphorylation and other post-translational modifications. HR occurs only during S and G2 phase of the cell cycle and all three subunits of RPA contain phosphorylation sites. The exact set of HR-relevant phosphorylation sites of RPA is unknown. In this study, the phosphorylation sites of chromatin-bound RPA in S and G2 phase were identified. After DNA damage, phosphorylation included pSer4/8, pSer12, pThr21, pSer23 and pSer33 of RPA2. Phosphorylation of these sites increased with time after DNA damage. Using a general ATM/ATR phosphorylation antibody, only RPA2 had substantial pSer/pThr ATM/ATR signals. Additionally, pTyr was detected on RPA1 and RPA2 and was removed in response to DSBs, indicating the regulatory action of a phosphatase. A capillary isoelectric focusing immunoassay used under native conditions revealed in high resolution isoforms of the RPA heterotrimer in control and damaged cell lysates in G2. Strikingly, RPA is a phosphoprotein in control G2 cell lysates with up to 5 putative phospho-isoforms containing up to 7 phosphates. These isoforms include RPA2 pSer23 and pSer33 and RPA1 pTyr. DNA damaged lysates contained 9 isoforms, containing up to 14 phosphates. DNA damage isoforms contained RPA2 pSer4/8, pSer12, pThr21, pSer23, pSer33 and other not yet identified phosphorylation sites.

Citation Format: Kerry Brader, Adam Mosel, Shengqin Liu, Elizabeth Kremmer, Kaitlin Goettsch, Heinz-Peter Nasheuer, Greg Oakley, Gloria Borgstahl. Interplay of DNA damage and cell cycle signaling on Replication Protein A in human cells. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Susceptibility and Cancer Susceptibility Syndromes; Jan 29-Feb 1, 2014; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(23 Suppl):Abstract nr 33. doi:10.1158/1538-7445.CANSUSC14-33
Abstract 34: Investigating PIN1 as a genetic modifier in Li-Fraumeni syndrome
Authors: Villani Anita , Novokmet Ana , Malkin David
Published: May 2015

Background: Li-Fraumeni syndrome (LFS) is characterized by marked clinical heterogeneity in site and age of cancer onset. The prolyl-isomerase, Pin1 (peptidylprolyl cis/trans isomerase, NIMA-interacting 1), has been shown to serve a fundamental role in mutant TP53 oncogenic gain of function and the promotion of aggressive cancer phenotypes. We sought to determine whether alterations in PIN1 modify the phenotype of patients with germline mutations in TP53.

Methods: The PIN1 promoter and coding regions were sequenced from peripheral blood lymphocyte samples of 107 individuals with Li-Fraumeni syndrome and documented TP53 mutations. The expression and activity levels of PIN1 were determined in paired patient-derived lymphoblastoid cell lines.

Results: Multivariate analysis of PIN1 variants with TP53 mutation status and selected clinical parameters is in progress. A comprehensive summary of observed associations will be presented.

Conclusions: Demonstration of a modifying effect of PIN1 on the cancer phenotype conferred by a germline TP53 mutation may aid in the management of patients with Li-Fraumeni syndrome, including the implementation of patient-specific modifications of surveillance strategies for pre-symptomatic tumor detection.

Citation Format: Anita Villani, Ana Novokmet, David Malkin. Investigating PIN1 as a genetic modifier in Li-Fraumeni syndrome. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Susceptibility and Cancer Susceptibility Syndromes; Jan 29-Feb 1, 2014; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(23 Suppl):Abstract nr 34. doi:10.1158/1538-7445.CANSUSC14-34