Abstract LB-317: Use of in vivo microdialysis to evaluate biomarker levels in the tumor and tumor free flank of freely-moving PDX mice

The tumor microenvironment (TME) constitutes unique surroundings where cancer cells communicate with one another and with the host immune system by releasing a multitude of factors. Information about the physiological state of the TME can help in gaining a broader understanding of cancer biology and developing novel cancer therapeutics. Previous work has demonstrated the ability to use in vivo microdialysis to monitor the release of adenosine and its metabolites from murine cancer models. To further these findings, we used in vivo microdialysis to measure biomarkers in the patient-derived xenograft (PDX) cancer model. By using human tumor tissue models, we aim to bridge the gap between rodent models and human tumors to help develop better cancer therapeutics.

The current set of studies used microdialysis in different PDX lines representing human tumor models (provided by CRL DRS Freiburg). Xenograft growth was monitored and upon a tumor volume > 400 mm3, the animals underwent surgical implantation of microdialysis probes in the tumor and the tumor-free flank. The implanted probes were perfused with dialysate fluid and samples from the both flanks were continuously collected over several hours. Levels of ATP, inosine and kynurenine metabolites were quantified by EIA or LC-MS/MS analysis.

Analysis of microdialysate samples from tumor and tumor-free flank demonstrated differences in analyte levels between the two sampling sites within one animal indicating that the levels of ATP and metabolites measured in PDX tumors is unique to the tumor microenvironment. In addition, the various PDX models showed differences in biomarker levels between the different tumor types. There is a wide range of biomarkers which are important indicators of energy consumption and provide an insight in the differences in metabolic activity between the different xenografts. Moreover, these data demonstrate that microdialysis can be used to test targeted therapies and follow relevant biomarker levels over time. Thereby, providing better insight in effects of new therapeutic treatments within the patient specific tumor tissue itself.

Citation Format: Mariette Heins, Loreen Weichert, Sabine Gorynia, Gunnar Flik, Arash Rassoulpour. Use of in vivo microdialysis to evaluate biomarker levels in the tumor and tumor free flank of freely-moving PDX mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-317.

In vitro efficacy of cold atmospheric pressure plasma on S. sanguinis biofilms in comparison of two test models

Dental plaque critically affects the etiology of caries, periodontitis and periimplantitis. The mechanical removal of plaque can only be performed partially due to limited accessibility. Therefore, plaque still represents one of the major therapeutic challenges. Even though antiseptic mouth rinses reduce the extent of biofilm temporarily, plaque removal remains incomplete and continuous usage can even result in side effects. Here we tested argon plasma produced by kinpen09 as one option to inactivate microorganisms and to eliminate plaque. S. sanguinis biofilms cultivated in either the European Biofilm Reactor (EUREBI) or in 24 well plates were treated with argon plasma. In both test systems a homogeneous, good analyzable and stable biofilm was produced on the surface of titan plates within 72 h (>6,9 log10 CFU/ml). Despite the significantly more powerful biofilm production in EUREBI, the difference of 0.4 log10 CFU/ml between EUREBI and the 24 well plates was practically not relevant. For that reason both test models were equally qualified for the analysis of efficacy of cold atmospheric pressure plasma. We demonstrate a significant reduction of the biofilm compared to the control in both test models. After plasma application of 180 s the biofilm produced in EUREBI or in 24 well plates was decreased by 0.6 log10 CFU/ml or 0.5 log10 CFU/ml, respectively. In comparison to recently published studies analyzing the efficacy of kinpen09, S. sanguinis produces a hardly removable biofilm. Future investigations using reduced distances between plasma source and biofilm, various compositions of plasma and alternative plasma sources will contribute to further optimization of the efficacy against S. sanguinis biofilms.

Abstract 3835: Ex vivo 3D assay: rapid and reliable replication of the in vivo anti-tumor efficacy of c-Met inhibitors

For compounds directed against molecular targets expressed in tumor cells, the ex vivo 3D tumor clonogenic assay (TCA) is a rapid and reliable ex vivo assay with a high predictive value for in vivo tumor sensitivity. Single cell suspensions prepared from patient-derived tumor xenografts (PDX) growing subcutaneously in nude mice or from cultured human tumor cell lines are seeded in semisolid medium and tumor colony formation is monitored in the presence or absence of test compounds over a period of one to three weeks.

Based on experiments with up to 70 PDX, we have demonstrated that the TCA accurately replicates the in vivo sensitivity of PDX towards cMet inhibitors across all major tumor histologies. More specifically, all three NSCLC PDX that regressed in response to cMet inhibition in in vivo efficacy tests were sensitive to several cMet inhibitors in the ex vivo TCA. By contrast, data obtained with a 2D cell proliferation and survival assay did not correlate with the 3D and in vivo situations, suggesting that cMet function does not affect cell survival and proliferation on plastic but confers the capacity for anchorage-independent growth. The correlation of 3D but not 2D data with in vivo sensitivity was confirmed using anti-cMet siRNAs in selected PDX-derived non-small cell lung cancer cell lines. Preliminary immunohistochemical analysis revealed that PDX sensitive to cMet inhibitors expressed high cMet levels while not all PDX expressing high cMet levels were sensitive to cMet inhibitors.

In conclusion, for cMet inhibitors the TCA replicates in vivo sensitivities of PDX to a high degree. Due to its short duration the TCA is an excellent tool for the screening of large numbers of cMet inhibitors and PDX. As all of the PDX qualified for use in the TCA (>200) have been extensively molecularly characterised (gene expression, gene copy number variation and mutation analysis) this assay is also an excellent tool for generating high quality biomarker hypotheses during the preclinical profiling of molecules intended for oncology indications.

Citation Format: Sabine Gorynia, Jianing Guo, Andreas Ackermann, Armin Maier, Rebekka Krumbach, Gerhard Kelter, Vincent Vuaroqueaux, Thomas Metz, Thomas Metcalfe, Heiner H. Fiebig. Ex vivo 3D assay: rapid and reliable replication of the in vivo anti-tumor efficacy of c-Met inhibitors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3835. doi:10.1158/1538-7445.AM2013-3835

Yeast Irc6p is a novel type of conserved clathrin coat accessory factor related to small G proteins

Yeast Irc6p is a novel type of conserved clathrin coat accessory protein that functions in clathrin-mediated traffic between the trans-Golgi network and endosomes, linking clathrin adaptor complex AP-1 and the Rab GTPase Ypt31p. Irc6p and the mammalian homologue p34 are founding members of a new G protein–like family.

Clathrin coat accessory proteins play key roles in transport mediated by clathrin-coated vesicles. Yeast Irc6p and the related mammalian p34 are putative clathrin accessory proteins that interact with clathrin adaptor complexes. We present evidence that Irc6p functions in clathrin-mediated traffic between the trans-Golgi network and endosomes, linking clathrin adaptor complex AP-1 and the Rab GTPase Ypt31p. The crystal structure of the Irc6p N-terminal domain revealed a G-protein fold most related to small G proteins of the Rab and Arf families. However, Irc6p lacks G-protein signature motifs and high-affinity GTP binding. Also, mutant Irc6p lacking candidate GTP-binding residues retained function. Mammalian p34 rescued growth defects in irc6∆ cells, indicating functional conservation, and modeling predicted a similar N-terminal fold in p34. Irc6p and p34 also contain functionally conserved C-terminal regions. Irc6p/p34-related proteins with the same two-part architecture are encoded in genomes of species as diverse as plants and humans. Together these results define Irc6p/p34 as a novel type of conserved clathrin accessory protein and founding members of a new G protein–like family.

Cloning, expression, purification, crystallization and preliminary X-ray analysis of the human RuvBL1-RuvBL2 complex

The complex of RuvBL1 and its homologue RuvBL2, two evolutionarily highly conserved eukaryotic proteins belonging to the AAA(+) (ATPase associated with diverse cellular activities) family of ATPases, was co-expressed in Escherichia coli. For crystallization purposes, the flexible domains II of RuvBL1 and RuvBL2 were truncated. The truncated RuvBL1-RuvBL2 complex was crystallized using the hanging-drop vapour-diffusion method at 293 K. The crystals were hexagonal-shaped plates and belonged to either the orthorhombic space group C222(1), with unit-cell parameters a = 111.4, b = 188.0, c = 243.4 A and six monomers in the asymmetric unit, or the monoclinic space group P2(1), with unit-cell parameters a = 109.2, b = 243.4, c = 109.3 A, beta = 118.7 degrees and 12 monomers in the asymmetric unit. The crystal structure could be solved by molecular replacement in both possible space groups and the solutions obtained showed that the complex forms a dodecamer.

Crystal structure of the human AAA+ protein RuvBL1

RuvBL1 is an evolutionarily highly conserved eukaryotic protein belonging to the AAA(+)-family of ATPases (ATPase associated with diverse cellular activities). It plays important roles in essential signaling pathways such as the c-Myc and Wnt pathways in chromatin remodeling, transcriptional and developmental regulation, and DNA repair and apoptosis. Herein we present the three-dimensional structure of the selenomethionine variant of human RuvBL1 refined using diffraction data to 2.2A of resolution. The crystal structure of the hexamer is formed of ADP-bound RuvBL1 monomers. The monomers contain three domains, of which the first and the third are involved in ATP binding and hydrolysis. Although it has been shown that ATPase activity of RuvBL1 is needed for several in vivo functions, we could only detect a marginal activity with the purified protein. Structural homology and DNA binding studies demonstrate that the second domain, which is unique among AAA(+) proteins and not present in the bacterial homolog RuvB, is a novel DNA/RNA-binding domain. We were able to demonstrate that RuvBL1 interacted with single-stranded DNA/RNA and double-stranded DNA. The structure of the RuvBL1.ADP complex, combined with our biochemical results, suggest that although RuvBL1 has all the structural characteristics of a molecular motor, even of an ATP-driven helicase, one or more as yet undetermined cofactors are needed for its enzymatic activity.

Expression, purification, crystallization and preliminary X-ray analysis of the human RuvB-like protein RuvBL1

RuvBL1, an evolutionary highly conserved protein related to the AAA+ family of ATPases, has been crystallized using the hanging-drop vapour-diffusion method at 293 K. The crystals are hexagonal and belong to space group P6, with unit-cell parameters a = b = 207.1, c = 60.7 A and three molecules in the asymmetric unit.