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Gene-based therapeutics; bioinformatics and systems biology; hepatocyte differentiation; novel strategies for treatment of brain tumorsOur work falls under a broad umbrella of Molecular Bioengineering: developing an understanding of molecular interactions in a biological context and exploiting this knowledge for the improved design of bioengineered products. This encompasses activities crossing interdisciplinary boundaries and including elements of biophysics. synthetic chemistry. engineering thermodynamics and kinetics. cell and molecular biology. and physiology. Examples of ongoing and possible projects are outlined briefly below. Molecular Bioengineering of Antisense OligonucleotidesThe sequencing of the human genome is more or less completed. with the promise of great improvements in understanding of human biology and concomitant advances in diagnosis and treatment of disease. Several technologies have emerged to inhibit the expression of specific target genes based on their gene sequence. We are working towards overcoming some of the technical barriers to two of the most promising -- antisense oligonucleotides (AS ONs) and short interfering RNAs (siRNAs). In one project. we have developed a molecular thermodynamic model of DNA:RNA binding that we are using to rationally design AS ONs of high affinity and rapid hybridization kinetics. and we are now investigating the extension of this methodology to siRNA design. In a second project. we use cell-specific ligands and biocompatible polymers to delivery oligonucleotides to cells with improved efficiency and selectivity. Genomics and Proteomics of Hepatic FunctionEfforts to develop "magic bullet" molecular therapeutics have been largely unsuccessful. in large part due to poor understanding of the underlying molecular basis for the disease being treated. Most physiological processes and disease conditions involve the concerted actions of large sets of genes. which may act synergistically. antagonistically. or in sophisticated feedback loops. We use computational and experimental approaches to analyze systems of molecules holistically. in an effort to rationally guide molecular strategies for engineering cell function. One application of this approach is the manipulation of transcription factor expression to confer differentiated function to cultured hepatocytes for tissue engineering applications. Another is the use of promoter binding site preferences and gene expression profiling to analyze dynamic responses of the liver to inflammatory stress. Selected PublicationsYang H, Roth CM, Ierapetritou MG. (2009) A rational design approach for amino acid supplementation in hepatocyte culture. Biotechnol Bioeng. Apr 3. [Epub ahead of print] Waite CL, Sparks SM, Uhrich KE, Roth CM. (2009) Acetylation of PAMAM dendrimers for cellular delivery of siRNA. BMC Biotechnol. 9:38. Roth CM. (2008) Quantitative measurements and rational materials design for intracellular delivery of oligonucleotides. Biotechnol Prog. 24(1):23-8. Sundaram S, Lee LK, Roth CM. (2007) Interplay of polyethyleneimine molecular weight and oligonucleotide backbone chemistry in the dynamics of antisense activity. Nucleic Acids Res. 35(13):4396-408. Lee LK, Dunham BM, Li Z, Roth CM. (2006) Cellular dynamics of antisense oligonucleotides and short interfering RNAs. Ann N Y Acad Sci. 1082:47-51. Lee LK. Williams CL. Devore D. Roth CM. (2006) Poly(propylacrylic acid) enhances cationic lipid-mediated delivery of antisense oligonucleotides. Biomacromolecules. 7(5):1502-8. Sundaram S. Viriyayuthakorn S. Roth CM. (2005) Oligonucleotide structure influences the interactions between cationic polymers and oligonucleotides. Biomacromolecules. 6(6):2961-8. Katz JM. Roth CM. Dunn MG. (2005) Factors that influence transgene expression and cell viability on DNA-PEI-seeded collagen films. Tissue Eng. 11(9-10):1398-406. Roth CM. (2005) Molecular and cellular barriers limiting the effectiveness of antisense oligonucleotides. Biophys. J. 89(4):2286-95. Gevertz JL. Dunn SM. Roth CM. (2005) Mathematical model of real-time PCR kinetics. Biotechnol. Bioeng. 92(3):346-55 Jayaraman A. Yarmush ML. Roth CM. (2005) Evaluation of an in vitro model of hepatic inflammatory response by gene expression profiling. Tissue Eng. 11:50-63. Roth CM. Sundaram S. (2004) Engineering synthetic vectors for improved DNA delivery: Insights from intracellular pathways. Annu. Rev. Biomed. Engr. 6:397-426. Lee LK and Roth CM. (2003) Antisense technology in molecular and cellular bioengineering. Curr. Opin. Biotechnol. 14:505-511. Roth CM. (2002) Quantifying gene expression. Curr. Issues Mol. Biol. 4:93-100. Walton SP. Stephanopoulos GN. Yarmush ML. Roth CM. (2002) Thermodynamics and kinetics of antisense oligonucleotide binding. Biophys J. 82:366-377. Jayaraman A. Yarmush ML. Roth CM. (2002) Molecular bioengineering Ind. & Eng. Chem. Res. 41:441-455. Jayaraman A. Walton SP. Yarmush ML. Roth CM. (2001). Rational selection and quantitative evaluation of antisense oligonucleotides. Biochim. Biophys. Acta 1520:105-114. |
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