bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract C62: Targeting cancer cell migration and invasion by immunomodulation of actin binding proteins using single domain antibodies (nanobodies)
Authors: De Ganck Ariane , Delanote Veerle , Van den Abbeele Anske , De Clercq Sarah , Vandekerckhove Joël , Gettemans Jan 
Published: May 2012

Abstract
Enhanced motility of cancer cells by remodeling of the actin cytoskeleton through the concerted actions of different classes of actin binding proteins is crucial in the process of cancer cell invasion and metastasis. It is therefore not surprising that expression of quite a few actin associated proteins like gelsolin, myopodin and plastin, fluctuates during tumorigenesis. Furthermore, many studies using overexpression or RNA interference showed a direct involvement of these structural proteins in malignant cell behavior.
Specific inhibitors of most cytoskeletal proteins are lacking. In an attempt to fill this gap, we developed Camelid single domain antibodies (nanobodies or VHHs) against several actin binding proteins including myopodin, gelsolin, and L-plastin. Recombinant nanobodies were used for the biophysical and biochemical characterization of their properties. Furthermore, we used intracellular expression of these nanobodies as intrabodies to develop functional protein domain ‘knock-outs’ to answer the question how ablation of a biochemical property of a protein translates into changes in cell morphology and cell behavior.
Results on gelsolin and L-plastin nanobodies show that they can bind their target antigen with nanomolar affinity in vitro. Cellular assays (for instance a mitochondrial outer membrane recruitment assay) were further used to confirm the interaction between the VHH intrabody and the endogenous antigen in vivo. Epitope mapping revealed for each nanobody to which domain of the protein they bind, demonstrating their selective interaction with different (conformational) epitopes.
In this way we isolated a gelsolin nanobody that only recognizes the activated, calcium-bound conformation of gelsolin. In contrast, other gelsolin nanobodies bind to gelsolin both in the presence and absence of calcium. Functional actin binding assays led to the identification of a gelsolin nanobody that blocks actin monomer binding. Furthermore, this nanobody is also able to reduce the motility of MDA-MB231 breast cancer cells.
A nanobody that specifically interacts with the tandem actin binding domains in L-plastin inhibits actin bundling in vitro. This ‘knock-out’ nanobody inhibits filopodia formation, motility and invasion when expressed in PC-3 prostate cancer cells. Remarkably, L-plastin RNA interference (RNAi) showed no significant effect on filopodial integrity.
In conclusion, single domain VHHs represent a potent tool to ablate protein function and to explore the cellular role of distinct biochemical activities of polypeptides without manipulating gene expression. Furthermore, they can evolve into new therapeutics for cancer treatment targeting currently ‘undruggable’ proteins.
Citation Information: Cancer Res 2009;69(23 Suppl):C62.
Abstract C66: A novel technique to quantify condensation/decondensation status in the nuclear subdomains by QD-FRET
Authors: Shaheen Sharif Mohammad , Akita Hidetaka , Yamashita Atsushi , Katoono Ryo , Yui Nobuhiko , Biju Vasudevanpillai , Ishikawa Mitsuru , Harashima Hideyoshi 
Published: May 2012

Abstract
Recent studies have reported that control of nuclear decondensation at specific nuclear subdomains (i.e. euchromatin) is highly desired for the efficient transfection efficiency. Here, we have established a novel technology for the imaging of nuclear condensation/decondensation status in the nuclear subdomains (i.e. heterochromatin and euchromatin) by based on the three key technologies.
One is imaging of fluorescence resonance energy transfer (FRET) between quantum dots (QDs)-labeled plasmid DNA (pDNA) as a donor, and acceptor-labeled polycation, which can monitor a specific molecular interactions at the nanometre scale.
The second technology is a multilayered lipid envelope-type nanoparticle, which we refer to as a Tetra-lamellar Multi-functional Envelope-type Nano Device (T-MEND). The critical structural elements of the T-MEND are a DNA—polycation condensed core coated with two nuclear membrane-fusogenic inner envelopes and two endosome-fusogenic outer envelopes, which are designed for nuclear delivery via a stepwise fusion. It is required to evaluate the nuclear dispositions in relation to the transgene expression, to avoid a situation that intracellular trafficking processes rate-limit transfection activity.
The last one is confocal image-assisted 3-dimensionally integrated quantification (CIDIQ) method. In this method, fluorophore-labeled pDNA was transfected in HeLa cell line, and then intracellular distribution was distinguished by staining organelle. Z-series of confocal images were captured by confocal laser scanning microscopy (CLSM), and thereafter, pDNA was quantified based on the pixel area of the signals derived from the fluorophore on pDNA in nuclear subdomains (heterochromatin and euchromatin).
As a model of the analysis, QD-labeled DNA was condensed with reductive environment-dependently cleavable polyrotaxane (DMAE-ss-PRX), an artificial condenser, and encapsulated in T-MEND. As a result, transfection activity depends on the number of cationic DMAE of cyclodextrin (α-CD), in conjunction with a drastic change in decondensation efficiency in euchromatin region. These data collectively indicate that this imaging technology is highly advantageous to clarify the dynamics of plasmid DNA in post-nuclear delivery process of cancer cells.
Citation Information: Cancer Res 2009;69(23 Suppl):C66.
Abstract C70: Rapid viscosity-based diagnostic for hyperviscosity in leukemia patients
Authors: van Nimwegen Lena , Hurth Cedric , Zenhausern Frederic 
Published: May 2012

Abstract
The rapid viscosity-based diagnostic test is designed to determine a method by which whole blood viscosity can be clinically tested, in a manner that is both time and cost effective. Leukemia, as well as other blood cell diseases such as Waldenstrom's macroglobulinemia, is associated with hyperviscosity, due to an increase in particular components of blood. Our goal is to use high speed video imaging to characterize the rheological properties of a whole blood sample in order to qualitatively determine the viscosity of the sample. Previous reports used rapid video imaging to describe the mechanics of fluid flow upon impact by a solid sphere (C. Duez et al, Nature Physics 2007, 3, 180–183). The primary method of characterization relies upon the determination of a threshold impact velocity at which the resulting splash profile transitions from a blob to a jet. We performed preliminary tests using a series of glycerol dilutions to mimic potential differences in blood viscosity. Glass beads (2mm diameter) were dropped with a variety of impact velocities into the glycerol solutions. The impact and the resulting splash were recorded using a high-speed camera (Olympus iSPEED 2) at 8000 frames per second. These tests indicated that different viscosities result in different threshold velocities at which the jet splash profile becomes apparent. We are reporting different methods of enrichment of whole blood in order to induce controlled changes in the viscosity of the samples that mimic physiological processes. We have adapted existing methods for enrichment of red blood cell membranes with cholesterol to create a condition known as “spur” red cells which is known to cause a decrease in red cell deformability, altering the visco-elastic properties of the cell (M. Shinitzky, FEBS Letters, 85, 317–320). The splash diagnostic test will be applied to these samples to determine the changes in viscosity resulting from the enrichment. Ultimately, we will test blood samples from leukemia patients at different stages of treatment to further improve the ability of the splash test to be used in a clinical environment.
Citation Information: Cancer Res 2009;69(23 Suppl):C70.
Abstract C72: A mechanistic link between whole-chromosome aneuploidy and DNA damage
Authors: Crasta Karen , Nezi Luigi , Hennessy Morgan , Cameron Lisa , Pan Yunfeng , Chowdhury Dipanjan , Pellman David 
Published: May 2012

Abstract
Cancer is associated with aneuploidy— both structural defects in chromosomes and abnormal numbers of intact chromosomes. The contribution of chromosome breaks to tumorigenesis is well accepted because of the possibility of generating cancer-causing mutations. However, the role of alterations of intact chromosome numbers remains a subject of debate, principally because mechanisms by which whole chromosome aneuploidy would affect cancer pathogenesis are poorly understood. We now have evidence to support one mechanism by which whole chromosome aneuploidy can lead to DNA breaks, via mis-segregation of chromosomes into micronuclei, structures commonly observed in cancer cells. Micronuclei containing intact chromosomes can form after mitotic errors, when the nuclear envelope reforms around a lagging chromosome. We have developed procedures to monitor the fate of micronuclei. Strikingly, whole chromosome-containing micronuclei develop evidence of DNA breaks during the first S phase after they are formed. Blocking DNA replication blocks the formation of these breaks. Defective DNA replication may be due to defective nucleocytoplasmic transport because micronuclei display a marked defect in assembling nuclear pore complexes. These findings suggest one mechanism by which mitotic errors result in DNA damage and thus potentially promote tumorigenesis.
Citation Information: Cancer Res 2009;69(23 Suppl):C72.
Abstract IA-10: Examining the scale and scope of tools and programs to navigate in translational oncology space: Lessons learned
Authors: Friend Stephen H. 
Published: May 2012

Abstract
Over the past five years extensive coherent data has been assembled into probabilistic causal models of diseases. These models show the potential power of generating larger and more comprehensive models. Leveraging significant datasets generated by the Genetics group at Rosetta, the compute clusters, and know-how, we have launched a non-profit commons called Sage based at the Fred Hutchinson Cancer Research Center. We will work to generate 1) a repository of coherent global datasets with genetic information, intermediate markers, and clinical outcomes capable of generating probabilistic causal models of disease, 2) the tools and architecture required to combine data sets and the interoperability required for use of multiple tools, 3) the hosting and curation of diverse disease models as generated by the community and 4) the governance and rules required for this to become a “commons” where open access enables a contributor network. New directions and examples of these models will be discussed.
Citation Information: Cancer Res 2009;69(23 Suppl):IA-10.
Abstract IA-11: Discovery and preclinical activity of IPI-926, a Hedgehog pathway inhibitor
Authors: Adams Julian 
Published: May 2012

Abstract
Malignant activation of the Hedgehog (Hh) pathway plays a key role in multiple types of human tumors, supporting the development of Hedgehog pathway antagonists as therapeutics for cancer. This pathway involves two cell-membrane proteins, Patched (Ptc) and Smoothened (Smo), and is regulated by the absence or presence of Hh ligand. Smo can promote growth of certain cancers via three modes of malignant activation of the Hh pathway: ligand-dependent signaling either to the tumor cell itself or from the tumor to its microenvironment, and ligand-independent signaling activated by genetic mutation. Smo has a critical role in the malignant activation of the Hh pathway because it initiates a signal transduction cascade that can result in cell differentiation, migration, and proliferation. Cyclopamine, a plant Veratrum alkaloid, is a natural product antagonist of the Hh pathway. Efforts to improve the pharmaceutical properties and potency of cyclopamine led to the discovery of IPI-926, a novel semi-synthetic analogue that inhibits the Hh pathway by binding to Smo. IPI-926 demonstrates excellent oral bioavailability, a long plasma half-life and duration of action, and is highly distributed to tumor tissue. Daily oral administration of IPI-926 results in dose-dependent inhibition of tumor growth in multiple preclinical models of cancer. Following tumor debulking in a primary human xenograft SCLC model with a chemotherapy treatment regimen similar to that used clinically in patients with SCLC, once-daily oral administration of IPI-926 leads to a statistically significant delay in tumor regrowth. In certain cancers including pancreatic and ovarian cancer, the tumor cells produce Hh ligand that diffuses out to the surrounding stroma and binds Ptc, resulting in Smo-mediated Hh pathway activation. This paracrine mode of Hh activation leads to recruitment, growth, and maintenance of the stromal tissue in the tumor microenvironment that supports tumor growth. In a genetically engineered murine model of pancreatic cancer, IPI-926 treatment results in depletion of tumor-associated stroma and prolonged survival when given in combination with gemcitabine. Because Smo plays a critical role in malignant activation of the Hh pathway in both the tumor and the stromal microenvironment, Smo may be a target for the management of a broad range of cancers. IPI-926 is currently being investigated in a Phase 1 clinical trial.
Citation Information: Cancer Res 2009;69(23 Suppl):IA-11.
Abstract IA-15: Balancing quiescence and proliferation in stem cells and its implications for cancer
Authors: Fuchs Elaine V. 
Published: May 2012

Abstract
Even though many adult tissues undergo relatively infrequent turnover, they still require stem cells (SCs) which are then used sparingly to replenish cells during normal homeostasis. Moreover, in response to injury, adult SCs must be mobilized quickly to repair damaged tissue. How SCs balance their ability to rest during periods of quiescence, activate to replenish cells and tissue when needed and replace the SCs used for tissue maintenance and repair are fascinating topics in stem cell biology and tissue morphogenesis. Moreover, increasing evidence suggests that the regulatory circuitry governing this balancing act is at the root of some types of tumors both in mice and in humans.
The skin is an excellent model system to understand how undifferentiated SCs self-renew to generate the epidermis and its notable appendages, hair follicles (HFs). In the embryo, skin begins as a single layer of multipotent progenitors, which adhere to each other as well as to an underlying basement membrane rich in extracellular matrix. These progenitors express members of the Lef1/Tcf family of DNA binding proteins thought to act as bipartite transcription factors in association with β-catenin. Excess β-catenin not utilized in intercellular junctions is stabilized when skin progenitors receive Wnt signals from their microenvironment to initiate HF formation. As development proceeds, progenitors respond to additional signals as the skin epithelial tissues mature and differentiate. Postnatally, epidermis retains SCs to undergo homeostasis and maintain the body surface barrier, while HFs undergo cyclical bouts of Wnt signaling that leads to follicle regeneration and hair growth, followed by destruction of the follicle and a resting period to accumulate a new threshold level of signal. The role of Wnt signaling in follicle SC activation and hair regeneration is particularly interesting, as mounting evidence suggests that Wnt signaling may play a general role in governing SC biology and injury repair.
Using skin as our paradigm, we have continued to dissect how extrinsic signaling to SCs sets off a cascade of changes in transcription that govern the activation of SCs during tissue development, homeostasis and hair cycling. We've focused our efforts on the roles of three Tcf/Lef1 family members, all expressed initially in the single-layered epithelium, but which then diversify to be differentially expressed in adult skin SCs and rapidly dividing but committed progeny. Our findings point to Wnt-independent as well as Wnt-dependent functions for these transcription factors, which are likely to be important for our understanding of why Wnt signaling is deregulated in a variety of different human cancers and how Wnt circuitry balances quiescence and proliferation in stem cell and progenitor compartments.
Citation Information: Cancer Res 2009;69(23 Suppl):IA-15.
Abstract IA-16: Control of growth by mTOR signaling
Authors: Sabatini David M. 
Published: May 2012

Abstract
mTOR is the target of the immunosuppressive drug rapamycin and the central component of a nutrient- and hormone-sensitive signaling pathway that regulates cell growth and proliferation. We now appreciate that this pathway becomes deregulated in many human cancers. We have identified two distinct mTOR-containing proteins complexes, one of which regulates growth through S6K and another that regulates cell survival through Akt. These complexes, mTORC1 and mTORC2, define both rapamycin-sensitive and insensitive branches of the mTOR pathway. I will discuss new results from our lab on the regulation of the mTORC1 and mTORC2 pathways. I will provide an overview of mTOR signaling as well as discuss the regulation of mTORC1 by insulin and nutrients and the role of mTORC2 in cancer. We have recently identified new upstream components of the mTORC1 pathway that are involved in amino acid sensing and are starting to understand some of the molecular mechanisms involved in this process. Current evidence suggests that amino acids regulate the mTORC1 pathway by controlling the intracellular localization of mTORC1. Specifically, amino acids promote the movement of mTORC1 to a part of the endomembrane system that also contains its activator Rheb. Amino acids signal through the conserved Rag family of small GTPases that directly interact with the raptor component of mTORC1 in fashion that depends on the GTP-loaded status of the Rags. In addition, I will present evidence that inhibition of mTORC1 by the novel mTOR-interacting protein Deptor is a mechanism for hyperactivating PI3K signaling in multiple myeloma.
Citation Information: Cancer Res 2009;69(23 Suppl):IA-16.
Abstract IA-17: The roles of prolyl hydroxylases in metabolism and cancer
Authors: Gottlieb Eyal 
Published: May 2012

Abstract
Both succinate dehydrogenase (SDH) and fumarate hydratase (FH) are Krebs cycle enzymes that convert succinate to fumarate and fumarate to malate, respectively. SDH is also a functional member (complex II) of the Electron Transport Chain. Surprisingly, although SDH and FH are ‘housekeeping genes’ with key bioenergetic roles, germline mutations in these genes cause cancer. We demonstrated that succinate, a Krebs cycle metabolite (an SDH substrate), functions as an intracellular messenger between mitochondria and the cytosol. Succinate, which accumulates in mitochondria due to the inactivation of SDH, leaks out to the cytosol, where it inhibits the enzymatic machinery of oxygen sensing, mediated by a family of α-ketoglutarate-dependent Prolyl Hydroxylase enzymes (PHD). PHD inhibition by succinate triggers the accumulation and activation of the hypoxia inducible factor (HIF) in the nucleus and the pseudohypoxic response that enhances tumour vascularisation and glycolysis. These and other independent studies collectively suggested that PHD inhibition and pseudohypoxia are important factors that link mitochondrial tumour suppressors and cancer. This observation received further support recently from the fact that PHD2 was genetically identified as a tumour suppressor.
The inhibition of PHD by succinate is achieved by a product inhibition mechanism, given that PHD hydroxylates its targets while utilizing α-ketoglutarate as a substrate and producing succinate. We further characterized the nature of succinate-mediated inhibition of PHD and showed that this inhibition is competitive in nature. Therefore, the ratio, rather than the absolute concentrations, of α-ketoglutarate to succinate or fumarate in cells critically affect PHD activity and HIF activity. We designed and synthesised cell-permeating α-ketoglutarate esters that are hydrolyzed in the cytosol by esterases. These compounds support PHD activity thereby lowering HIF levels and activity in SDH deficient cells. Furthermore, we also demonstrated that α-ketoglutarate increased the affinity of PHD to oxygen and reactivate PHD in cells under hypoxia, resulting in destabilization of the HIFα proteins. It is likely that the binding of α-ketoglutarate by PHD ‘primes’ the enzyme for the binding of oxygen. Our study suggests that well-designed α-ketoglutarate derivatives may have therapeutic potential in the treatment of tumors with functional down-regulation of oxidative phosphorylation. Furthermore, the functional consequences of the observations that PHDs are sensors for oxygen and α-ketoglutarate will be discussed.
Citation Information: Cancer Res 2009;69(23 Suppl):IA-17.
Abstract IA-19: Deconstructing metastasis
Authors: Massagué Joan 
Published: May 2012

Abstract
Metastasis is a multi-stage process that selects for circulating cancer cells that can infiltrate, survive in, and colonize distant organs. The cellular origin, oncogenic alterations, tissue affinities, and circulation patterns of tumors markedly influence the sites and temporal course of metastasis. Cancer cell dissemination may be followed by a protracted period of latency before relapse in one or more organs, as in breast cancer, or by a swift colonization of multiple organs, as in lung adenocarcinoma. We have sought to incorporate this varied biology into experimental models to deconstruct metastasis. Searching for mechanisms that prime breast cancer cells for infiltration of different organs, we found few requirements for cancer cell extravasation through fenestrated bone marrow capillaries, certain key requirements (EGFR ligands, COX2, TGFβ-induced angiopoietin-like 4) for infiltration through the non-fenestrated walls of lung and brain capillaries, and additional mediators (sialyl transferase ST6GalNac5) for infiltration though brain capillaries with blood-brain barrier. Searching for mechanisms that allow infiltrated breast cancer cells to survive as latent disease, we found that a hyperactive SRC pathway supports the responsiveness of breast cancer cells to certain survival factors in the marrow microenvironment. Searching for mechanisms that in contrast underlie the rapid metastasis of lung adenocarcinomas to brain and bone, we uncovered an involvement of WNT/TCF signaling through HOXH9 and LEF1. These striking disparities in the natural progression of different cancers bring into focus important questions about the evolution of metastatic traits, the molecular mediators involved, and the treatment opportunities for the prevention of metastasis.
Citation Information: Cancer Res 2009;69(23 Suppl):IA-19.
Abstract IA-2: PI3-Kinase and cancer metabolism
Authors: Cantley Lewis C. 
Published: May 2012

Abstract
Mutations in Phosphoinositide 3-Kinase (PI3K) are among the most common events in solid tumors. Recent studies have revealed a highly conserved pathway by which PI3K regulates cell growth and glucose metabolism. Mice with activating mutations in the PIK3CA gene develop cancers that have high rates of glucose uptake and metabolism and pharmacological inhibitors of PI3K block glucose uptake and cause tumor shrinkage. We have also shown that the embryonic form of pyruvate kinase plays a critical role in tumor cell growth by diverting glucose metabolites into anabolic processes. The biochemical basis for these observations and their importance for tumor growth will be discussed.
Citation Information: Cancer Res 2009;69(23 Suppl):IA-2.