Biotechnologies for cancer diagnostics : cell sorting, protein analysis and imaging of cellular metabolism

This thesis presents the development of chip-based technology for informative in vitro cancer diagnostics. In the first part of this thesis, I will present my contribution in the development of a technology called “Nucleic Acid Cell Sorting (NACS)”, based on microarrays composed of nucleic acid encoded peptide major histocompatibility complexes (p/MHC), and the experimental and theoretical methods to detect and analyze secreted proteins from single or few cells.

Secondly, a novel portable platform for imaging of cellular metabolism with radio probes is presented. A microfluidic chip, so called “Radiopharmaceutical Imaging Chip” (RIMChip), combined with a beta-particle imaging camera, is developed to visualize the uptake of radio probes in a small number of cells. Due to its sophisticated design, RIMChip allows robust and user-friendly execution of sensitive and quantitative radio assays. The performance of this platform is validated with adherent and suspension cancer cell lines. This platform is then applied to study the metabolic response of cancer cells under the treatment of drugs. Both cases of mouse lymphoma and human glioblastoma cell lines, the metabolic responses to the drug exposures are observed within a short time (~ 1 hour), and are correlated with the arrest of cell-cycle, or with changes in receptor tyrosine kinase signaling.

The last parts of this thesis present summaries of ongoing projects: development of a new agent as an in vivo imaging probe for c-MET, and quantitative monitoring of glycolytic metabolism of primary glioblastoma cells. To develop a new agent for c-MET imaging, the one-bead-one-compound combinatorial library method is used, coupled with iterative screening. The performance of the agent is quantitatively validated with cell-based fluorescent assays. In the case of monitoring the metabolism of primary glioblastoma cell, by RIMChip, cells were sorting according to their expression levels of oncoprotein, or were treated with different kinds of drugs to study the metabolic heterogeneity of cancer cells or metabolic response of glioblastoma cells to drug treatments, respectively.

Studies of molecular bonding, interactions and decomposition reactions on the (001) surface of ruthenium

The interactions of N₂, formic acid and acetone on the Ru(001) surface are studied using thermal desorption mass spectrometry (TDMS), electron energy loss spectroscopy (EELS), and computer modeling.

Low energy electron diffraction (LEED), EELS and TDMS were used to study chemisorption of N₂ on Ru(001). Adsorption at 75 K produces two desorption states. Adsorption at 95 K fills only the higher energy desorption state and produces a (√3 x √3)R30° LEED pattern. EEL spectra indicate both desorption states are populated by N₂ molecules bonded "on-top" of Ru atoms.

Monte Carlo simulation results are presented on Ru(001) using a kinetic lattice gas model with precursor mediated adsorption, desorption and migration. The model gives good agreement with experimental data. The island growth rate was computed using the same model and is well fit by R(t)^m - R(t₀)^m = At, with m approximately 8. The island size was determined from the width of the superlattice diffraction feature.

The techniques, algorithms and computer programs used for simulations are documented. Coordinate schemes for indexing sites on a 2-D hexagonal lattice, programs for simulation of adsorption and desorption, techniques for analysis of ordering, and computer graphics routines are discussed.

The adsorption of formic acid on Ru(001) has been studied by EELS and TDMS. Large exposures produce a molecular multilayer species. A monodentate formate, bidentate formate, and a hydroxyl species are stable intermediates in formic acid decomposition. The monodentate formate species is converted to the bidentate species by heating. Formic acid decomposition products are CO₂, CO, H₂, H₂O and oxygen adatoms. The ratio of desorbed CO with respect to CO₂ increases both with slower heating rates and with lower coverages.

The existence of two different forms of adsorbed acetone, side-on, bonded through the oxygen and acyl carbon, and end-on, bonded through the oxygen, have been verified by EELS. On Pt(111), only the end-on species is observed. On dean Ru(001) and p(2 x 2)O precovered Ru(001), both forms coexist. The side-on species is dominant on clean Ru(001), while O stabilizes the end-on form. The end-on form desorbs molecularly. Bonding geometry stability is explained by surface Lewis acidity and by comparison to organometallic coordination complexes.

Thermodynamic and kinetic behavior of an argon plasma jet. Decomposition of nitric oxide between 1300 - 1750 degrees K in an argon plasma

In the first part of the study, an RF coupled, atmospheric pressure, laminar plasma jet of argon was investigated for thermodynamic equilibrium and some rate processes.

Improved values of transition probabilities for 17 lines of argon I were developed from known values for 7 lines. The effect of inhomogeneity of the source was pointed out.

The temperatures, T, and the electron densities, n_e , were determined spectroscopically from the population densities of the higher excited states assuming the Saha-Boltzmann relationship to be valid for these states. The axial velocities, v_z, were measured by tracing the paths of particles of boron nitride using a three-dimentional mapping technique. The above quantities varied in the following ranges: 10¹² ˂ n_e ˂ 10¹⁵ particles/cm³, 3500 ˂ T ˂ 11000 °K, and 200 ˂ v_z ˂ 1200 cm/sec.

The absence of excitation equilibrium for the lower excitation population including the ground state under certain conditions of T and n_e was established and the departure from equilibrium was examined quantitatively. The ground state was shown to be highly underpopulated for the decaying plasma.

Rates of recombination between electrons and ions were obtained by solving the steady-state equation of continuity for electrons. The observed rates were consistent with a dissociative-molecular ion mechanism with a steady-state assumption for the molecular ions.

In the second part of the study, decomposition of NO was studied in the plasma at lower temperatures. The mole fractions of NO denoted by x_NO were determined gas-chromatographically and varied between 0.0012 ˂ x_NO ˂ 0.0055. The temperatures were measured pyrometrically and varied between 1300 ˂ T ˂ 1750°K. The observed rates of decomposition were orders of magnitude greater than those obtained by the previous workers under purely thermal reaction conditions. The overall activation energy was about 9 kcal/g mol which was considerably lower than the value under thermal conditions. The effect of excess nitrogen was to reduce the rate of decomposition of NO and to increase the order of the reaction with respect to NO from 1.33 to 1.85. The observed rates were consistent with a chain mechanism in which atomic nitrogen and oxygen act as chain carriers. The increased rates of decomposition and the reduced activation energy in the presence of the plasma could be explained on the basis of the observed large amount of atomic nitrogen which was probably formed as the result of reactions between excited atoms and ions of argon and the molecular nitrogen.

Part I. Regulation of development in the cellular slime mold Dictyostelium discoideum. Part II. Polysomes and RNA synthesis during early development of the surf clam Spisula solidissima

Part I. The cellular slime mold Dictyostelium discoideum is a simple eukaryote which undergoes a multi-cellular developmental process. Single cell myxamoebae divide vegetatively in the presence of a food source. When the food is depleted or removed, the cells aggregate, forming a migrating pseudoplasmodium which differentiates into a fruiting body containing stalk and spore cells. I have shown that during the developmental cycle glycogen phosphorylase, aminopeptidase, and alanine transaminase are developmentally regulated, that is their specific activities increased at a specific time in the developmental cycle. Phosphorylase activity is undetectable in developing cells until mid-aggregation whereupon it increases and reaches a maximum at mid-culmination. Thereafter the enzyme disappears. Actinomycin D and cycloheximide studies as well as studies with morphologically aberrant and temporally deranged mutants indicate that prior RNA and concomitant protein synthesis are necessary for the rise and decrease in activity and support the view that the appearance of the enzyme is regulated at the transcriptional level. Aminopeptidase and alanine transaminase increase 3 fold starting at starvation and reach maximum activity at 18 and 5 hours respectively.

The cellular DNA s of D. discoideum were characterized by CsC1 buoyant density gradient centrifugation and by renaturation kinetics. Whole cell DNA exhibits three bands in CsCl: ρ = 1.676 g/cc (nuclear main band), 1.687 (nuclear satellite), and 1.682 (mitochondrial). Reassociation kinetics at a criterion of Tm -23°C indicates that the nuclear reiterated sequences make up 30% of the genome (Cot_1/2 (pure) 0.28) and the single-copy DNA 70% (Cot_1/2(pure) 70). The complexity of the nuclear genome is 30 x 10⁹ daltons and that of the mitochondrial DNA is 35-40 x 10⁶ daltons (Cot_1/2 0.15). rRNA cistrons constitute 2.2% of nuclear DNA and have a ρ = 1.682.

RNA extracted from 4 stages during developmental cycle of Dictyostelium was hybridized with purified single-copy nuclear DNA. The hybrids had properties indicative of single-copy DNA-RNA hybrids. These studies indicate that there are, during development, qualitative and quantitative changes in the portion of the single-copy of the genome transcribed. Overall, 56% of the genome is represented by transcripts between the amoeba and mid-culmination stages. Some 19% are sequences which are represented at all stages while 37% of the genome consists of stage specific sequences.

Part II. RNA and protein synthesis and polysome formation were studied during early development of the surf clam Spisula solidissima embryos. The oocyte has a small number of polysomes and a low but measurable rate of protein synthesis (leucine-³H incorporation). After fertilization, there is a continual increase in the percentage of ribosomes sedimenting in the polysome region. Newly synthesized RNA (uridine-5-³H incorporation) was found in polysomes as early as the 2-cell stage. During cleavage, the newly formed RNA is associated mainly with the light polysomes.

RNA extracted from polysomes labeled at the 4-cell stage is polydisperse, nonribosomal, and non-4 S. Actinomycin D causes a reduction of about 30% of the polysomes formed between fertilization and the 16-cell stage.

In the early cleavage stages the light polysomes are mostly affected by actinomycin.