Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2005. / Includes bibliographical references. / The extracellular matrix of tumors is a major barrier to the delivery of molecular medicine. We used fluorescence recovery after photobleaching combined with intravital microscopy to quantitate the transport properties of the tumor interstitium. We found that the presence of fibrillar collagen correlated with hindered diffusion in vivo, and also in vitro, in collagen gels prepared to mimic tumor extracellular matrix. Modification of the tumor collagen matrix directly with purified bacterial collagenase, or indirectly with relaxin treatment, resulted in increased diffusion coefficients of macromolecules within tumors in vivo. In order to quantitate the changes in collagen content and structure induced by relaxin treatment, we adapted and further developed the imaging technique of intravital second harmonic generation microscopy. Using second harmonic generation imaging in combination with a fluorescently labeled gene therapeutic vector, we demonstrated that the spread of these viral vectors within tumors is limited by the fibrillar collagen in the extracellular matrix. Matrix modification via the introduction of bacterial collagenase along with the initial virus injection resulted in a significant improvement in the range of viral distribution within the tumor. / (cont.) This resulted in an extended range of infection of cells within the tumor, and improved virus propagation, ultimately leading to enhanced therapeutic outcome. Thus, we show that fibrillar collagen is an important barrier to the distribution of molecular medicine within tumors, and that matrix modifying treatments can significantly enhance both vector distribution, as well as ultimately therapeutic response. / by Trevor David McKee. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2004. / Includes bibliographical references (leaves 124-140). / Understanding the hepatotoxicity of drugs and chemicals is essential for progress in academic research, medical science and in the development of new pharmaceuticals. Studying hepatotoxicity in vitro is a challenging task because hepatocytes, the metabolically active cells of the liver, are very difficult to maintain in culture. After just 24 hours, the cells detach from the plate and die, and even if they survive they usually do not express the metabolic functions which they have in vivo. It has been observed by others that culturing hepatocytes between two layers of collagen type I maintains in vivo-like morphology and also many drug metabolizing enzymes for weeks. In spite of the research examining drug metabolism in collagen sandwiches, there are very few studies evaluating this system for investigating hepatotoxicity. We cultured primary rat hepatocytes in the collagen sandwich configuration and our goal was to optimize this system for long-term studies and to examine toxicity of a variety of hepatotoxins. By measuring secretions of urea and albumin, and P4501A activity, we determined the optimal cell density to be 50,000 cells/cm2. We also evaluated the need for epidermal growth factor (EGF) in our cultures, by comparing urea and albumin secretions in cultures grown with and without EGF. The cultures without EGF had significantly less secretion of both urea and albumin just two days after plating. Therefore, we decided to include EGF in the medium. The toxins we examined were aflatoxin B1, acetaminophen, carbon tetrachloride, N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), methyl methane sulfonate (MMS), cadmium, vinyl acetate and dimethylformamide (DMF). The cells were sensitive to aflatoxin B1, MMS, MNNG and cadmium. However, they were / (cont.) immune to acetaminophen, carbon tetrachloride, vinyl acetate and DMF. Our Western Blots showed that CYP1A, 2B and 3A were maintained in the culture for a week, but CYP2E1 was lost gradually over time. CYP2E1 is also the primary metabolic enzyme for acetaminophen, carbon tetrachloride and DMF. Thus, it is possible that the lack of toxicity is due to the loss of the enzyme responsible for the metabolism of these compounds. Immunity to vinyl acetate suggests that carboxylesterase is also lost in culture, since this enzyme is the one which converts vinyl acetate to acetaldehyde. The metabolism of acetaminophen was also examined with liquid chromatography and mass spectrometry. Liquid chromatography showed that acetaminophen is metabolized primarily to the sulfate and glucuronide metabolites. In order to investigate whether the glutathione adduct was formed, we synthesized the adduct and determined its retention time with liquid chromatography and its fragmentation pattern with mass spectrometry. We isolated the fraction with the same retention time from the medium of acetaminophen-treated cells, and showed that it contains a peak with the same mass to charge ratio and fragmentation pattern as the glutathione adduct. We also examined the conditioned medium from the hepatocytes to investigate the secreted protein profile, which could potentially be used to find toxicity biomarkers. We were able to remove most of the albumin from the medium using an immuno-affinity column containing anti-albumin antibodies bound to protein A-agarose beads ... / by Dóra Farkas. / Ph.D.

Thesis (M. Eng.)--Massachusetts Institute of Technology, Biological Engineering Division, 2004. / Includes bibliographical references (p. 70-73). / Comb polymer, which consists of a hydrophobic poly(methyl methacrylate) (PMMA) backbone with hydrophilic hydroxy-poly(ethylene oxide) (HPOEM) side chains, is a tool that has many possible applications for the study of liver cell adhesion and signaling. This polymer has the unique properties of being cell resistant and chemically versatile such that various cell ligands can be coupled to its side chains. These properties allow adhesion through specific cell receptors to be studied without the effect of background adhesion to adsorbed proteins. By taking advantage of the ability to target specific receptors the comb polymer could be used as a powerful sorting tool. Sorting could be accomplished by finding cell type specific adhesion ligands. Several possible such ligands were screened. A ligand containing the tripeptide sequence RGD was found to elicit a strong cell adhesion response. However, this ligand is adherent to many cell types of the liver and would not be suitable for sorting purposes. Other cell type specific ligands tested showed little to no affinity for liver cell adhesion. Additionally, the comb was utilized to study α₅β₁ integrin-specific hepatocyte adhesion and the effect of Epidermal Growth Factor on adhesion. α₅β₁ integrin adhesion was mediated using a novel branched peptide, SynKRGD. This peptide consists of a linear peptide sequence containing RGDSP and the synergy site sequence PHSRN connected by the sequence GGKGGG. By utilizing the amine side group of Lysine a GGC branch was added. The terminal cysteine was used to conjugate SynKRGD to comb polymer surfaces using N-(p-Maleimidophenyl) isocyanate (PMPI) chemistry. EGF has a great potential to benefit the field of tissue engineering due to its influence on cell / (cont.) proliferation, migration, and differentiation. EGF is also known to have a de-adhesive effect in some cell types. Hepatocytes were studied on comb surfaces of variable SynKRGD densities with and without the presence of EGF in the media. Distinct morphological differences were observed for hepatocytes on substrates of varying adhesivity with and without the presence of EGF. EGF was found to have a de-adhesive effect on α₅β₁ integrin adhesion in hepatocytes. This effect became more pronounced as substrate adhesiveness increased. / by David Yin. / M.Eng.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2004. / Includes bibliographical references. / (cont.) phosphoproteomics technology, IMAC/LC/MS/MS, [approximately] 200 phosphosites were identified from HT-29 cells, some of which were detected only from insulin-treated cells. Our phosphoproteomics approach also enabled us to detect alteration of both known and unknown phosphorylation states of apoptosis-related proteins at two time points during early apoptosis induced by tumor necrosis factor-α / Apoptosis, a physiologically regulated cell death, plays critical roles in development and immune system by maintaining tissue homeostasis. The thesis project investigates regulations of apoptosis in a human colon adenocarcinoma cell line, HT-29, exposed to diverse cellular stimuli, focusing on a specific protein as well as global level of proteins. The first part of the thesis demonstrated S-nitrosation of procaspase-9. S-nitrosation is a novel protein modification to regulate protein-protein interaction or protein activity. This modification has been implied to inactivate caspases. We could visualize S-nitrosation of an initiator caspase, procaspase-9, by enriching low-abundant procaspase-9 with immunoprecipitation and stabilizing S-nitroso-cysteine with biotin labeling. Nitric oxide synthase inhibitors and tumor necrosis factor-α (TNF-α) reduced the S-nitrosation level of procaspase-9, suggesting that S-nitrosation may be regulated by a nitric oxide synthase and denitrosation is likely a mechanism of apoptosis. The second part of the thesis is to examine survival effects of insulin on cells undergoing TNF-α-induced apoptosis. Insulin decreased the TNF-α-induced cleavage of key apoptotic mediators, caspases, and their substrates as well as apoptosis, in part, depending on phosphatidylinositol-3 kinase (PI-3K)/Akt pathway. One of protective mechanisms by insulin is likely to decrease the TNF-α-induced dissociation of a potent inhibitor of caspases, X-chromosome linked inhibitor of apoptosis protein (XIAP), from procaspase-9 via PI-3K/Akt pathway. Lack of phosphoproteomics data in HT-29 cells led the third part of the thesis to focus on investigating global level regulation of phosphoproteins during apoptosis. With a / by Ji-Eun Kim. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2007. / Includes bibliographical references. / Our understanding of glycosaminoglycan (GAG) biology has been limited by a lack of sensitive and efficient analytical tools designed to deal with these complex molecules. GAGs are heterogeneous and often sulfated linear polys accharides found throughout the extracellular environment, and available to researchers only in limited mixtures. A series of sensitive label-free analytical tools were developed to provide sequence information and to quantify whole epitopes from GAG mixtures. Three complementary sets of tools were developed to provide GAG sequence information. Two novel exolytic sulfatases from Flavobacterium heparinum that degrade heparan/heparan sulfate glycosaminoglycans (HSGAGs) were cloned and characterized. These exolytic enzymes enabled the exo-sequencing of a HSGAG oligosaccharide. Phenylboronic acids (PBAs) were specifically reacted with unsulfated chondroitin sulfate (CS) disaccharides from within a larger mixture. The resulting cyclic esters were easily detected in mass spectrometry (MS) using the distinct isotopic abundance of boron. Electrospray ionization tandem mass spectrometry (ESI-MSn) was employed to determine the fragmentation patterns of HSGAG disaccharides. These patterns were used to quantify relative amounts of isomeric disaccharides in a mixture. Fragmentation information is valuable for building methods for oligosaccharide sequencing, and the general method can be applied to quantify any isomers using MSn. Three other tools were developed to quantify GAG epitopes. Two microfluidic devices were characterized as HSGAG sensors. Sensors were functionalized either with protamine to quantify total HSGAGs or with antithrombin-III (AT-III) to quantify a specific anticoagulant epitope. / (cont.) A charge sensitive silicon field effect sensor accurately quantified clinically relevant anticoagulants including low molecular weight heparins (LMWH), even out of serum. A mass sensitive suspended microchannel resonator (SMR) measured the same clinically relevant HSGAGs. When these two sensors were compared, the SMR proved more robust and versatile. The SMR signal is more stable, it can be reused ad infinitum, and surface modifications can be automated and monitored. The field effect sensor provided an advantage in selectivity by preferentially detecting highly charged HSGAGs instead of any massive, non-specifically bound proteins. Lastly, anti-HSGAG single chain variable fragments (scFv) were evolved using yeast surface display towards generating antibodies for HSGAG epitope sensing and clinical GAG neutralization. / by Jonathan Robert Behr. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2007. / Includes bibliographical references. / The potential of gene therapy to treat disease and improve human health is tremendous. The failure of viral gene therapy clinical trials due to toxicity, immunogenicity, and carcinogenicity has been tragic and strongly motivates a non-viral approach. However, non-viral gene delivery is currently ineffective. Here, we show that polymeric nanoparticles composed of poly([beta]-amino esters) (PBAEs) and DNA can be formulated to be stable in the presence of serum proteins and have high gene delivery without toxicity to human primary cells. The biophysical properties of PBAE/DNA nanoparticles have good correlation to transfection efficacy when tested in the appropriate media conditions. We also show that electrostatic interactions can drive peptide coating of nanoparticles and enable ligand-specific gene delivery. A biphasic efficacy relationship exists for peptide weight ratio, overall charge ratio, and ligand length, with intermediate values of coating being optimal. A balance is required when seeking to design nanoparticles that have reduced nonspecific uptake, but increased ligand-specific uptake. We develop a high-throughput assay to quantify polymer/DNA binding as a gene delivery bottleneck and find that a biphasic relationship exists between polymer/DNA binding constant, Ka, and delivery efficacy. We also show that end-modified PBAEs can be as effective as adenovirus for gene delivery. In comparison to the previous "gold standard" for polymeric transfection, 25 kDa polyethylenimine, the PBAE nanoparticles presented here have 100x higher efficacy while simultaneously having 100x lower toxicity. Small structural changes were found to have dramatic effects on multiple steps of gene delivery including the DNA binding affinity, nanoparticle size, intracellular DNA uptake, and final protein expression. / (cont.) We show that small modifications to the termini of a polymer can significantly increase its in vivo activity and demonstrate potential utility of these polymers in the fields of cancer therapy, genetic vaccines, and stem cell engineering. As the enhanced polymeric gene delivery nanoparticles described here have many attractive properties over a virus including high safety, low immunogenicity, high nucleic acid cargo capacity, ease in manufacture, a coating method for targeted delivery, and flexibility for future design improvements, we believe that these polymeric nanoparticles may be promising alternatives for therapeutic gene delivery applications. / by Jordan Jamieson Green. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2006. / Includes bibliographical references (leaves 108-122). / Many liver physiological and pathophysiological behaviors are not adequately captured by current in vitro hepatocyte culture methods. A 3D perfused microreactor previously demonstrated superior hepatic functional maintenance than conventional 2D cultures, and was hypothesized to provide an environment favorable to endothelial cell maintenance and morphogenesis. This dissertation focuses on characterizing the 3D perfused co-culture of primary hepatocyte fraction with primary rat liver endothelial isolate. Scanning electron microscopy revealed significantly higher numbers of pore-like structures on the co-culture tissue surface resembling liver sinusoids compared to cultures containing only the hepatocytes fraction (mono-culture). EGFP-labeled endothelial cells proliferated moderately and organized into microvessel-like structures as observed by in situ multi-photon microscopy. By mixing female endothelial cells with male hepatocytes, the female cell population increased from initially -7% on day 1 to -12% on day 13, as determined by quantitative PCR on genomic DNA. The maintenance and morphogenesis of endothelial cells were not observed in parallel 2D collagen gel sandwich cultures. Immunohistochemistry further confirmed the presence of sinusoidal endothelia within the 3D co-culture tissue, as well as other non-parenchymal cells in both 3D mono-culture and co-culture. / (cont.) Global transcriptional profiling confirmed the loss of endothelia in 2D culture as the comparison between mono-culture and co-culture showed substantial differential expression levels only in the 3D format. The majority of the genes expressed substantially higher in 3D co-culture than mono-culture was found to be endothelia-specific. A group of key liver metabolism genes, however, do not show significant expression differences between the 3D cultures. This study concludes that the 3D perfused microreactor maintains non-parenchymal cells better than the 2D format, and the retention of non-parenchymal cells in the primary hepatocyte fraction likely contributes to the maintenance of key hepatic function gene expression. Additional endothelial cells organize into microvessel-like structures in this environment, but exert little influence on the gene expression of most key liver transcription factors and metabolism enzymes. Therefore 3D cultures may eliminate the need of co-cultures for applications focusing on metabolic behaviors of hepatocytes, and 3D endothelial-hepatocyte co-cultures may prove useful in studies where proper endothelium structure is required, such as cancer metastasis. / by Albert J. Hwa. / Ph.D.

Thesis (Ph. D. in Genetic Toxicology)--Massachusetts Institute of Technology, Biological Engineering Division, 2003. / Includes bibliographical references. / Although homologous recombination provides an efficient means for repairing and tolerating DNA damage, mitotic recombination between misaligned sequences can lead to loss of genetic information (e.g. deletions, translocations and loss of heterozygosity). Given that such genetic changes may promote tumorigenesis, it is critical to identify those genetic and environmental factors that render cells susceptible to homologous recombination. Our goal is to elucidate the mechanisms of DNA damage-induced recombination and to determine the role of DNA repair enzymes in modulating homologous recombination in eukaryotic cells. Alkylating agents are abundant in our environment and are generated endogenously as normal metabolites. In addition to their mutagenic and cytotoxic effects, alkylating agents stimulate homologous recombination in eukaryotic cells. Removal of alkylated bases by DNA glycosylases, such as the Magl 3-methyladenine (3MeA) DNA glycosylase, initiates the base excision repair (BER) pathway. To investigate the molecular basis for methylation-induced homologous recombination in S. cerevisiae, intrachromosomal recombination was measured under conditions where MAGI expression levels were varied. Cells lacking Magl show increased susceptibility to methylation-induced recombination, suggesting that unrepaired 3MeA lesions induce recombination. Overexpression of M4GI also elevates recombination levels, presumably due to the accumulation of recombinogenic BER intermediates. / (cont.) To study the relative importance of specific DNA repair enzymes in modulating recombination in mammals, we have engineered transgenic mice that make it possible to quantify homologous recombination events in primary somatic cells, both in vitro and in vivo. The FYDR (fluorescent yellow direct repeat) mice carry two different mutant copies of an expression cassette for enhanced yellow fluorescent protein (EYFP) arranged in a direct repeat. Homologous recombination between these truncated sequences restores expression of EYFP. Using flow cytometry, spontaneous and DNA damage-induced recombination events were quantified in primary fibroblasts cultured from embryonic and adult tissues. In addition, recombination events that occurred in vivo were detected directly in disaggregated skin cells. Currently, FYDR mice are being crossed with mice carrying engineered defects to determine how specific gene traits modulate susceptibility to mitotic recombination. Ultimately, this tool will help us better understand how environmental agents and specific genes influence cellular susceptibility to cancer-promoting recombination events in mammals. / by Carrie A. Hendricks. / Ph.D.in Genetic Toxicology

Thesis (Ph. D.)--Massachusetts Institute of Technology, Biological Engineering Division, 2006. / "June 2006." / Includes bibliographical references. / Glycans are chemically heterogeneous macromolecules that have profound importance in a variety of biological processes. Located at the surfaces of cells, deposited in the extracellular matrix, or attached to soluble signaling agents, these molecules are characterized by a structural complexity that has thus far prevented their widespread exploitation in biomedicine. Insight into the fine structure and sequence of these complex biomolecules provides a novel niche for the development of therapeutic interventions. Such an understanding is rapidly accumulating via the molecular cloning, recombinant genetic expression, and protein purification of glycosaminoglycan-degrading enzymes. To this end, enzymes from the chondroitinase family of Pedobacter heparinus and Proteus vulgaris were developed. This library of enzymatic tools will reveal glycoconjugate structure-function motifs, allowed for by structural elucidation of glycan species using coupled bioinformatics/analytical chemistry techniques centered on mass spectrometry, nuclear magnetic resonance, and capillary electrophoresis. / (cont.) Biochemical characterization of these enzymes has allowed for the rational genetic manipulation of substrate recognition and binding site amino acid residues, producing site-directed protein engineered mutants with altered action pattern and substrate specificity. Progress in these areas will allow for the elucidation of critical roles of glycans in the biological regulation of growth factors, morphogens, cytokines, and cell-surface proteins. This extension of the capabilities of glycan analytical biotechnologies will help to translate basic science glycobiology to applied glycomedicine and drug discovery. / by Vikas Prabhakar. / Ph.D.

Thesis (Ph. D. in Genetic Toxicology)--Massachusetts Institute of Technology, Biological Engineering Division, 2004. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (p. 139-161). / It is a widely-held hypothesis that environmental mutagens play an essential role in human somatic and germinal cell mutagenesis. In particular, the finding of small amounts of chemical mutagens in cigarette smoke has led to the general hypothesis that mutagens in cigarette smoke induce oncomutations and thus account for the carcinogenic effect of cigarette smoking in human lungs. However, this hypothesis has not been tested by an assay of nuclear point mutations in lungs of smokers and nonsmokers. Mismatch amplification mutation assay (MAMA), an effective form of allele-specific PCR, was applied for detection of point mutations in TP53 bp742, bp746 and bp747, K-ras bp35 and HPRT bp508 from a total of 291 tracheal-bronchial epithelial sectors from six smokers and nine non-smokers, yielding 949 individual mutational assays. The conditions of MAMA for each target point mutations were optimized such that the sensitivity of each was equal to or below 10⁻⁵. Lung epithelial sectors of 2.3x10⁶ cells in average contained 0-200 mutant cells in general, equivalent to mutant fractions (MFs) of 0-10⁻⁴ with an exception of rare sectors with MF larger than 4x 10⁻⁴ (4.6%). Noticeably, the distributions of the MFs among sectors did not vary appreciably with the donor's smoking status. The mean MFs per lung were very similar between smokers and non-smokers for all five target mutations assayed (p >> 0.05). The mean MFs were slightly higher in females than males (p = 0.015). The mean MFs increased with age of the subjects although the correlation did not reach statistical significance due to large variances within the same age group. The distributions of MF among sectors of smokers and non-smokers did not differ significantly by Kolmogorov-Smirnov test / (cont.) for all target mutations but HPRT. By using hypothetical turnover unit sizes and Poisson distribution, the turnover unit size of human tracheal bronchial epithelium was estimated as 64 cells (p = 0.05). These observations do not support the widely-held hypothesis that cigarette smoking causes lung cancer through its induction of point mutations in nuclear genes. The current findings demonstrate the necessity of investigation on alternative mechanisms for tobacco smoke in lung carcinogenesis. / by Hiroko Sudo. / Ph.D.in Genetic Toxicology