gene therapy methods

Preface Gene therapy is less than ten years old and still very much in its infancy The first clinical gene therapy study was carried out in 1995 by Blaese and colleagues Although early results on clinical efficacy were disappointing, the logic of gene therapy is irresistibly attractive As science continues to evaluate the prospects for gene therapy, so the clinical benefits have begun to be demonstrated Early results were hampered because of inadequate vectors for gene transfer Most of the clinical studies involved gene addition However, gene therapy allows both correction and replacement of defective genes Ultimately, the goal is to have an in vivo somatic gene therapy that can deal with not only immediate life-threatening diseases, such as cancer and AIDS, but also chronic diseases that reduce the quality of life, such as hypertension and inflammatory diseases The basis for gene therapy is understanding which genes are involved in diseased phenotypes and which vectors are appropriate for providing therapeutic genes The rapid progress in gene discovery has been accelerated by the completion of the human genome project This book brings together, for the first time, methods in gene therapy that reflect the development of scientifically grounded systems for delivering genes DNA can be engineered to carry a therapeutic gene in sufficient quantities for full-scale clinical trials The methods can be classified as either viral or nonviral Viral vectors are replication defective viruses with part of their coding sequences replaced by the therapeutic gene These viral vectors include retroviruses, adenovirus, adenoassociated virus, herpes simplex viruS, papillomavirus, and lentivirus Nonviral vectors are simpler and easier to produce on the large scale However, each has its advantage Viral vectors can be engineered to be expressed in specific tissue and only under specific conditions Nonviral vectors are less easy to control so precisely Some diseases need gene therapy for a rapid effect, such as killing off tumor cells Others need the presence of a stable, safe gene delivery system for chronic lifetime diseases The use of gene therapy could eliminate the need for repeated administrations, improved therapeutic efficacy, and fewer side effects In hypertension, for example, one of the major problems is the lack of patient compliance in taking current prescribed drugs that have to be administered once a day The prospect of prolonged effective control of blood pressure and the subsequent reduction in heart attacks, stroke, and end-stage renal disease are an exciting possibility of the true benefits of gene therapy In this book we have brought together some of the leading researchers and research methods in gene therapy There are many ways to classify these chapters: by disease, by the type of method, or the type of delivery system We have chosen xix xx METHODS IN ENZYMOLOGY to classify them under the main type of delivery system being investigated However, each chapter stands on its own, offering scientific insight and experience with a particular approach In some cases they cross the boundaries of these classifications Although this is the first volume entitled "Gene Therapy Methods" for the Methods in Enzymology series, the increasing number of new methods and the progress of gene therapy will undoubtedly require more volumes in the future I wish to thank the authors for their contributions I also wish to thank Ms Gayle Butters of the University of Florida, Department of Physiology and Functional Genomics, for her excellent editorial assistance My thanks also go to Shirley Light of Academic Press for her encouragement to this volume M IAN PHILLIPS Contributors to V o l u m e Article numbers are in parentheses following the names of contributors Affiliations listed are current ANDREW H BAKER (10), Department of J BRANDEN (6), Center for BioTechnology, Department of BiDsciences, Karolinska Institute, SE-141 57 Huddinge, Sweden t EARS Medicine and Therapeutics, University of Glasgow, Glasgow GI1 6NT, United Kingdom PARAMITA BANDYOPADHYAY (2), ValiGen, Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, Massachusetts 02129 XANDRA BREAKEFIELD (34), Inc., Newtown, Pennsylvania 18940 ANDREA BANFI (9), Department of Molec- ular Pharmacology, Stanford University School of Medicine, CCSR 4215, Stanford, California 94305 J S BROMBERG (12), Institute for Gene Therapy and Molecular Medicine, Mount Sinai School of Medicine, New York, New York 10029 CATHERINE BARJOT (13), Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109* VLADIMIR BUDKER (7), Departments of Pe- diatrics and Medical Genetics, University of Wisconsin, Madison, Wisconsin 53705 ARTHUR L BEAUDET (11), Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas 77030 MARK M BURCIN (31), Cardiogene, 40699 Erkrath, Germany HELEN M BEAU (9), Department of Molec- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309 MASSlMO BUVOLI (8), ular Pharmacology, Stanford University School of Medicine, CCSR 4215, Stanford, California 94305 E BOROS (12), Institute for Gene Therapy CHERYL A CARLSON (16), Department and Molecular Medicine, Mount Sinai School of Medicine, New York, New York 10029 of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195 O BOYER (17), Laboratoire de Biologie et M G CASTRO (17), Molecular Medicine Thgrapeutique des Pathologies Immunitaires, Universit~ Pierre et Marie Curie, HOpital de la Piti#-Salp~tri#re, 75651 Paris Cedex 13, France and Gene Therapy Unit School of Medicine, University of Manchester, Manchester M13 9PT, United Kingdom~ *Current affiliation: UMR INRA 703, ENVN Atlanpole La Chanterie, F-44307 Nantes Cedex 3, France t Current affiliation: Clinical Research Center, Karolinska Institute, S-141 86 Stockholm, Sweden Current affiliation: Gene Therapeutics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048 xi xii CONTRIBUTORS TO VOLUME 346 JEFFREY S CHAMBERLAIN (13), Depart- BEVERLY L DAVIDSON (25), Depart- ment of Neurology, University of Washington School of Medicine, Seattle, Washington 98195 ments of Internal Medicine, Neurology, Physiology, and Biophysics, College of Medicine, University of lowa, Iowa City, Iowa 52242 JULIE CHAO (14), Department of Biochem- istry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425 LEE CHAO (14), Department of Biochem- istry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425 MICHELEDE PALMA(29), Institute for Can- cer Research and Treatment, Laboratory for Gene Transfer and Therapy, University of Torino Medical School 10060 Candiolo, Torino, Italy Y DING (12), Institute for Gene Therapy and KYE CHESNUT (24), Powell Gene Ther- Molecular Medicine, Mount Sinai School of Medicine, New York, New York 10029 apy Center, University of Florida, Gainesville, Florida 32610 J KEVINDONAHUE(19), Institute of Molec- JAYANTA ROY CHOWDHURY (2), Depart- ment of Medicine and Molecular Genetics, and Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, New York 10461 NAMITAROY CHOWDHURY(2), Department of Medicine and Molecular Genetics, and Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, New York 10461 YI CHU (15), Cardiovascular Division, University of lowa College of Medicine, Iowa City, Iowa 52242 ular Cardiobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 JIAN-YUN DONG (30), Department of Mi- crobiology, Medical University of South Carolina, Charleston, South Carolina 29425 DONGSHENG DUAN (20), Department of Anatomy and Cell Biology, University of Iowa College of Medicine, Iowa City, Iowa 52242 FIONAM ELLARD(27), Department of BiD- chemistry, Oxford BioMedica (UK) Limited, Oxford OX4 4GA, United Kingdom MARINEE K L CHUAH (33), Flanders JOHN E ENGELHARDT(20), Department of Interuniversity Institute of Biotechnology, Center for Transgene Technology and Gene Therapy, University of Leuven, B-3000 Leuven, Belgium Anatomy and Cell Biology, University of Iowa College of Medicine, Iowa City, Iowa 52242 DESIRE COLLEN (33), Flanders Interuni- versity Institute of Biotechnology, Center for Transgene Technology and Gene Therapy, University of Leuven, B-3000 Leuven, Belgium PIETER R CULLIS (3), Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3, and Inex Pharmaceuticals Corporation, Burnaby, Canada V5J 5L8 DAVID B FENSKE (3), Department of Bio- chemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3 TERRY FLOTTE (24), Powell Gene Ther- apy Center, University of Florida, Gainesville, Florida 32610 ANTONIAFOLLENZI(26), IRCC, Institute for Cancer Research and Treatment, Laboratory for Gene Transfer and Therapy, University of Torino Medical School 10060 Candiolo, Torino, Italy CONTRIBUTORS TO VOLUME 346 xiii CORNEL FRAEFEL (34), Institute of Virology, WILLIAM W HAUSWIRTH (21), Depart- University of Zurich, CH-8057 Zurich, Switzerland JASON J FRITZ (21), Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610 S Fu (12), Institute for Gene Therapy and Molecular Medicine, Mount Sinai School of Medicine, New York, New York 10029 MARK R GALLAGHER (23), Harvard/ G~ngthon Joint Laboratory, Harvard Institutes of Medicine, Boston, Massachusetts 02115 CRAIG H GELBAND (32), Department of Physiology, University of Florida College of Medicine and Functional Genomics, Gainesville, Florida 32610 C A GERDES (l 7), Molecular Medicine and Gene Therapy Unit School of Medicine, University of Manchester, Manchester M13 9PT, United Kingdom* ment of Ophthalmology and Powell Gene Therapy Center, College of Medicine, University of Florida, Gainesville, Florida 32610 GLASSPOOL-MALONE (4), Gene Delivery Alliance, Inc., Rockville, Maryland 20850 JILL JOHN T GRAY (23), Harvard/G~n~thon Joint Laboratory, Harvard Institutes of Medicine, Boston, Massachusetts 02115 WALTER H GiJNZBURG(35), Institute of Vi- rology, University of Veterinary Sciences, A-1210 Vienna, Austria YUTAKA HANAZONO (22), Division of Ge- netic Therapeutics, Center for Molecular Medicine, Jichi Medical School, Kawachi, Tochigi 329-0498, Japan KRISTINE HANSON (7), Departments of Pe- diatrics and Medical Genetics, University of Wisconsin, Madison, Wisconsin 53705 DENNIS HARTIGAN-O'CONNOR (13), De- partment of Neurology, University of Washington School of Medicine, Seattle, Washington 98195 DONALD D HEISTAD (15), Cardiovascular Division, University of Iowa College of Medicine, Iowa City, Iowa 52242 MIKKO O HILTUNEN (18), University of Kuopio, A L Virtanen Institute, FIN-70210 Kuopio, Finland MATTHEW J HUENTELMAN (32), Department of Physiology and Functional Genomics, College of Medicine, University of Florida, Gainesville, Florida 32610 NEIL JOSEPHSON (37), Division of Hematology, University of Washington, Seattle, Washington 98195 YASUFUMI KANEDA (36), Division of Gene Therapy Science, Graduate School of Medicine, Osaka University, Suita City, Osaka 565-0871, Japan MICHAEL J KATOVICH (32), Department of Physiology and Functional Genomics, College of Medicine, University of Florida, Gainesville, Florida 32610 NOBUFUMI KAWAI (22), Department of Physiology, Jichi Medical School, Kawachi, Tochigi 329-0498, Japan SUSAN M K1NGSMAN(27), Department of Biochemistry, Oxford BioMedica (UK) Limited, Oxford OX4 4GA, United Kingdom D KLATZMANN (17), Laboratoire de Bi- ologie et Th~rapeutique des Pathologies lmmunitaires, Universit~ Pierre et Marie Curie, CNRS, HOpital de la Pitig-Salpgtrigre, 75651 Paris Cedex 13, France Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota 55455 BETSY T KREN (2), *Current affiliation: GlycArt Biotechnology AG, 8093 Zurich, Switzerland xiv CONTRIBUTORS TO VOLUME 346 T KU (12), Institute for Gene Therapy IAN MACLACHLAN (3), Protiva Biother- and Molecular Medicine, Mount Sinai School of Medicine, New York, New York 10029 apeutics, Burnaby, British Columbia, Canada V5J 5L8 ROBERT W MALONE (4), Gene Delivery AKIHIRO KUME (22), Division of Ge- Alliance, Inc., Rockville, Maryland 20850 netic Therapeutics, Center for Molecular Medicine, Jichi Medical School Kawachi, Tochigi 329-0498, Japan LESLIE A LEINWAND (8), Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309 MICHELLE K LEPPO (19), Institute of Molecular Cardiobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 ALFRED S LEWIN (21), Department of Molecular Genetics and Microbiology, Powell Gene Therapy Center, College of Medicine, University of Florida, Gainesville, Florida 32610 LIEBER (16), Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195 ANDl~ DEXI LIU (5), Department of Pharmaceu- tical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania 15261 FENG LIU (5), Department of Pharmaceu- tical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania 15261 J.-MATTHIAS LOHR (35), Department of Institute of Molecular Cardiobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 ENCA MARTIN-RENDON (27), Department of Biochemistry, Oxford BioMedica (UK) Limited, Oxford OX4 4GA, United Kingdom EDUARDO MARB,~N (19), MATHEWS (23), Harvard/ Gdn(thon Joint Laboratory, Harvard Institutes of Medicine, Boston, Massachusetts 02115 TAKASHI MATSUSHITA (22), Division of Genetic Therapeutics, Center for Molecular Medicine, Jichi Medical School, Kawachi, Tochigi 329-0498, Japan NICHOLAS D MAZARAKIS (27), Department of Biochemistry, Oxford BioMedica (UK) Limited, Oxford OX4 4GA, United Kingdom PAUL B McCRAY, JR (28), Departments of Pediatrics and Internal Medicine, University of Iowa, Iowa City, Iowa 52242 KYRIACOS A MITROPHANOUS (27), Department of Biochemistry, Oxford BioMedica (UK) Limited, Oxford OX4 4GA, United Kingdom LYDIA C HIROAKI MIZUKAMI (22), Division of Ge- netic Therapeutics, Center for Molecular Medicine, Jichi Medical School, Kawachi, Tochigi 329-0498, Japan Molecular Gastroenterology, Medical Clinic II, University of Heidelberg, D-6816 Mannheim, Germany P RYUICHIMORISHITA(36), Division of Gene Molecular Medicine and Gene Therapy Unit School of Medicine, University of Manchester, Manchester M13 9PT, United Kingdom* NICHOLAS MUZYCZKA (24), Powell Gene R LOWENSTEIN (17), Therapy Science, Graduate School of Medicine, Osaka University, Suita City, Osaka 565-0871, Japan Therapy Center, University of Florida, Gainesville, Florida 32610 *Current affiliation: Gene Therapeutics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048 CONTRIBUTORS TO VOLUME 346 xv LUIGI NALD1NI (26, 29, 33), Institute for M IAN PHILLIPS (1), Department of Phys- Cancer Research and Treatment, Laboratory for Gene Transfer and Therapy, University of Torino Medical School, 10060 Candiolo, Torino, Italy iology and Functional Genomics, College of Medicine, University of Florida, Gainesville, Florida 32610 NATHALIE NEYROUD (19), Institute of Molecular Cardiobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 STUART A NICKLIN (10), Department of Medicine and Therapeutics, University of Glasgow, Glasgow Gll 6NT, United Kingdom TATSUYA NOMOTO (22), Division of Ge- netic Therapeutics, Center for Molecular Medicine, Jichi Medical School, Kawachi, Tochigi 329-0498, Japan JAMES S NORRIS (30), Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina 29425 n BRADLEYNUSS (19), Institute of Molec- ular Cardiobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205 TAKASHI OKADA (22), Division of Ge- netic Therapeutics, Center for Molecular Medicine, Jichi Medical School, Kawachi, Tochigi 329-0498, Japan BERT W O'MALLEY (31), Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030 KEIYA OZAWA (22), Division of Ge- netic Therapeutics, Center for Molecular Medicine, Jichi Medical School, Kawachi, Tochigi 329-0498, Japan Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas 77030* LucIo PASTORE (11), MARK POTTER (24), Powell Gene Ther- apy Center, University of Florida, Gainesville, Florida 32610 L QIN (12), Institute for Gene Therapy and Molecular Medicine, Mount Sinai School of Medicine, New York, New York 10029 PIPPA A RADCLIFFE (27), Department of Biochemistry, Oxford BioMedica (UK) Limited, Oxford OX4 4GA, United Kingdom MOHAN K RAIZADA (32), Department of Physiology and Functional Genomics, College of Medicine, University of Florida, Gainesville, Florida 32610 PHYLLIS Y REAVES (32), Department of Physiology, College of Medicine, University of Florida, GainesviUe, Maryland 32610 TERESA C RITCHIE (20), Department of Anatomy and Cell Biology, University of Iowa College of Medicine, Iowa City, Iowa 52242 JONATHAN B ROHLL (27), Department of Biochemistry, Oxford BioMedica (UK) Limited, Oxford OX4 4GA, United Kingdom Department of Microbiology, Medical University of South Carolina, Charleston, South Carolina 29425 SEMYON RUBINCHIK (30), DAVID W RUSSELL(37), Division of Hema- tology, University of Washington, Seattle, Washington 98195 ROBERT SALLER (35), Bavarian Nordic, D-82152 Martinsried, Austria BRIAN SALMONS (35), Austrian Nordic, A-1210 Vienna, Austria *Current affiliation: CEINGE-Biotecnologie Avanzate and Dipartimento di Biochima e Biotecnologie Mediche, Universit~t degli Studi di Napoli "Federico II," 80131 Napoli, Italy xvi CONTRIBUTORS TO VOLUME 346 GIOVANNI SALVATORI(13), Department of HARMUT STECHER (16), Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109* Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195 KURT SCHILLINGER (31), Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030 DMITRY M SHAYAKHMETOV(16), Depart- CLIFFORD J STEER (2), Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota 55455 ment of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195 COLLEEN S Department of Physiology, Center for Molecular Medicine, Jichi Medical School, Kawachi, Tochigi 329-0498, Japan DIRK S STEINWAERDER(16), Department PATRICKL SINN (28), Departments of Pedi- R SUNG (12), Institute for Gene Therapy atrics and Internal Medicine, Program in Gene Therapy, College of Medicine, University of Iowa, Iowa City, Iowa 52242 and Molecular Medicine, Mount Sinai School of Medicine, New York, New York 10029 Center for BioTechnology, Department of Biosciences, Karolinska Institute, SE-141 57 Huddinge, Sweden t C E THOMAS (17), Molecular Medicine SNYDER (23), Harvard/ G~n~thon Joint Laboratory, Division of Molecular Medicine, The Children's Hospital, Department of Pediatrics, Harvard Institutes of Medicine, Boston, Massachusetts 02115~ KIYOTAKE TOBITA (22), Department of KUNIKO SHIMAZAKI (22), C I EDVARD SMITH (6), RICHARD O Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania 15261 § YOUNG K SONG (5), MATTHEW L SPRINGER (9), Department of Molecular Pharmacology, Stanford University School of Medicine, CCSR 4215, Stanford, California 94305 STEIN (25), College of Medicine, University of lowa, Iowa City, Iowa 52242 of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington 98195 and Gene Therapy Unit School of Medicine, University of Manchester, Manchester M13 9PT, United Kingdom II Virology, Jichi Medical School, Kawachi, Tochigi 329-0498, Japan S TONDEUR (17), Laboratoire de Biologie et Th~rapeutique des Pathologies lmmunitaires, Universit~Pierre et Marie Curie, H~pital de la Piti~ Salp~tri~re 75651 Paris Cedex 13, France GRANT TROBRIDGE(37), Division of Hema- tology, University of Washington, Seattle, Washington 98195 SOPHIA Y TSAI (31), Department of Molec- ular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030 *Current affiliation: Department of Immunology, Sigma-Tau S.EA., 00040 Pomezia, Italy tCurrent affiliation: Clinical Research Center, Karolinska Institute, S-141 86 Stockholm, Sweden :~Current affiliation: Powell Gene Therapy Center, Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610 §Current affiliation: Department of Pharmacology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261 IICurrent affiliation: Department of Pediatrics and Genetics, Stanford University, Stanford, California 94305 CONTRIBUTORS TO VOLUME 346 xvii MIKKO P TURUNEN(18), A L Virtanen In- JIANLONG WANG (38), Lineberger Com- stitute, University of Kuopio, FIN-70210 Kuopio, Finland prehensive Cancer Center, University of North Carolina at Chapel Hill Chapel Hill, North Carolina 27599* P UMANA (17), Molecular Medicine and Gene Therapy Unit School of Medicine, University of Manchester, Manchester M13 9PT, United Kingdom* MASASHI URABE (22), Division of Ge- netic Therapeutics, Center for Molecular Medicine, Jichi Medical School Kawachi, Tochigi 329-0498, Japan THIERRY VANDENDRIESSCHE (33), Flan- ders lnteruniversity Institute of Biotechnology, Center for Transgene Technology and Gene Therapy, University of Leuven, B-3000 Leuven, Belgium GEORGE VASSILOPOULOS(37), Division of Hematology, University of Washington, Seattle, Washington 98195 SAM WANG (34), Molecular Neurogenet- ics Unit, Massachusetts General Hospital Charlestown, Massachusetts 02129 D ALANWHITE (21), Department of Molec- ular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida 32610 STEVE J WHITE (10), Department of Medicine and Therapeutics, University of Glasgow, Glasgow Gll 6NT, United Kingdom PHILLIP WILLIAMS (7), Departments of Pediatrics and Medical Genetics, University of Wisconsin, Madison, Wisconsin 53705 JON A WOLFF (7), Departments of Pediatrics and Medical Genetics, University of Wisconsin, Madison, Wisconsin 53705 T VERAKIS (17), Molecular Medicine and LORRAINE M WORK (10), Department of Gene Therapy Unit School of Medicine, University of Manchester, Manchester M13 9PT, United Kingdom Medicine and Therapeutics, University of Glasgow, Glasgow Gll 6NT, United Kingdom JEAN-MICHEL H VOS (deceased) (38), ZIYING YAN (20), Department of Anatomy Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 and Cell Biology, University of Iowa College of Medicine, Iowa City, Iowa 52242 XIANGUANGYE (31), Department of Molec- CINDY WANG (14), Departments of Bio- SEPPO YLX-HERTTUALA(18), Department chemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425 ular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030 of Molecular Medicine, A I Virtanen Institute, University of Kuopio, FIN-70210 Kuopio, Finland GUOSHUN WANG (28), Departments of Pe- JOSEPH ZABNER (28), Departments of Pe- diatrics and Internal Medicine, Program in Gene Therapy, College of Medicine, University of Iowa, Iowa City, Iowa 52242 t diatrics and Internal Medicine, Program in Gene Therapy, College of Medicine, University of Iowa, Iowa City, Iowa 52242 *Current affiliation: GlycArt Biotechnology AG, 8093 Zurich, Switzerland t Current affiliation: Departments of Medicine and Genetics, Gene Therapy Program, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112 *Current affiliation: Division of Hematology/Oncology, Children's Hospital Boston, Boston, Massachusetts 02115 xviii CONTRIBUTORS TO VOLUME 346 GUISHENG ZHANG (5), Department of HESHAN ZHOU (11), Cell and Gene Ther- Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania 15261 apy Center, Baylor College of Medicine, Houston, Texas 77030 GUOFENGZHANG(7), Departments of Pedi- atrics and Medical Genetics, University of Wisconsin, Madison, Wisconsin 53705 SERGEI ZOLOTUKHIN(24), Department of Molecular Genetics and Microbiology, Powell Gene Therapy Center, University of Florida, Gainesville, Florida 32610 714 SUBJECT INDEX production and purification, 283-284 titering, 284-285 stability of vectors, 292 hypertension gene therapy vectors, 11,247 kallikrein delivery in rats adenovirus preparation, 247-249 apoptosis assay, 256-257 blood pressure response, 259-260 blood vessel hyperplasia inhibition after balloon angioplasty, 261-262 cardiac function assay with fluorescent microspheres, 255-256 cardiomyocyte diameter response, 250-253 cardiovascular benefits, 260-261,263 expression level and time course, 259 rationale, 247 regional blood flow response, 254-255 renal hemodynamic effects, 253,261 superoxide histochemistry, 257-258 tissue distribution of transgene, 258-259 vector delivery routes carotid artery, 249 intracerebroventricular, 250 intramuscular, 249 intra-salivary gland, 250 intravenous injection, 249 organ transplantation gene transfer immune response, 213 liver gene transfer, 220, 222-223 overview, 201 receptor, 158, 160 second-generation vectors, 178 targeting strategies, 158, 160 tropism, 158, 247 /~l-Adrenoreceptor, antisense therapy of hypertension, ADRP, s e e Autosomal dominant retinitis pigmentosa ALS, s e e Amyotrophic lateral sclerosis Amyotrophic lateral sclerosis, gene mutations, 433-434 Angiogenesis myoblast-mediated gene transfer therapy controlled angiogenesis approach, 146-148 growth factors, 145-146 histochemical assessment, 154 vascular continuity assessment with fluorescent microbead perfnsion, 154-157 targeting of gene therapy, 165-166 Angiotensinogen, antisense therapy of hypertension, Angiotensin receptor type antisense delivery with Moloney marine leukemia virus delivery to neonatal rats, 567 hypertension effects in spontaneously hypertensive rat, 563, 567-569 large-scale production of virus, 566-567 packaging cell production, 563-565 titering of vector encoding drug resistance marker, 565-566 antisense therapy of hypertension, 8-9 receptor Antisense hemagglutinating virus of Japan-liposomes, antisense oligodeoxynucleotide uptake by cells, 621 hypertension gene therapy fll-adrenoreceptor antisense, angiotensinogen antisense, angiotensin receptor type antisense, 8-9, 563-567 antisense oligodeoxynucleotide delivery, 5-6, 12 overview of targets, 5, 13 viral vectors, a l-Antitrypsin, helper-dependent adenoviral vector delivery, 193-194 Apoptosis adenovirus vector induction challenges, 529, 531 Fas ligand-green fluorescent protein expression cell culture, 541-542 design of vector, 533-537 infectious particle titration, 543-544 large-scale production of vector, 544-545 ligation assembly of genome and transfection, 532-533,538-542 lysate preparation, 542-543 packaging cell line development expressing CrmA and Bcl2, 537-538 wild-type revertant detection, 546-547 packaging cell lines, 532 regulation of transgene expression, 531-532 SUBJECT INDEX hippocampus assay following ischemia and bcl-2 delivery, 391 kaUikrein delivery in rats and apoptosis assay, 256-257 Aurintricarboxylic acid endonuclease inhibition specificity, 75 lipoplex transfection efficiency effects in monkey lung, 75-76 mouse studies of gene transfer enhancement animals, 85 inhibitor preparation, 87 intratracheal plasmid instillation, 87-88 luciferase assay, 86-87 plasmid preparation, 86 nuclease inhibitor enhancement of gene delivery, rationale, 74-75 nucleic acid vaccine efficacy effects, 76-77 Autosomal dominant retinitis pigmentosa rhodopsin mutations, 361 ribozyme gene therapy adeno-associated virus vector packaging, 376-377 cleavage assay for hammerhead ribozyme long RNA targe transcription and cleavage time courses, 373-375 multiple turnover kinetic analysis, 370-373 RNA deprotection and phosphorylation, 368-369 time course analysis, 369-370 cloning of ribozymes and targets adeno-associated virus vector DNA purification, 366-368 oligonucleotide purification and phosphorylation, 366 overview, 365 materials, 362-363 rationale, 361-362 ribozyme design hairpin ribozyme, 364-365 hammerhead ribozyme, 363-364 target site identification, 363 t3 Balloon angioplasty, hyperplasia prevention with kallikrein gene delivery in ~ats, 261-262 Basic fibroblast growth factor, angiogenesis gene therapy, 145 715 B cell lymphoma, gene therapy with miniEBV vectors, 658-659 Bcl-2, gene delivery for ischemia-induced neuronal death with adeno-associated virus vector epitope tagging of transgene, 379-381 gerbil model hippocampal apoptosis assay, 391 histochemical analysis of epitope-tagged Bcl-2, 388-389, 391 injection of vector in brain, 387-388 ischemia induction, 384-385 rationale, 378-379 vector production with triple plasmid transfection materials, 382-383 principles, 381-382 purification, 384 transfection, 383 bFGF, see Basic fibroblast growth factor Bioplex, see Peptide nucleic acid Blood vessel, gene transfer adenoviral vectors advantages, 263-264 artery gene transfer ex vivo, 269-270 calcium phosphate coprecipitate for augmentation, 275-276 construction, 264-265 delivery routes in vivo adventitial delivery, 272-274 intraarterial delivery, 271-272 intracranial delivery, 274-275 fl-galactosidase reporter assay, 270 optimization of transgene expression, 267-268 propagation, 266-267 rabbit model /5-galactosidase reporter detection, 318-319 intravascular transfer, 315-316 overview, 313 periadventitial transfer, 316-317 tissue fixation, 318 ex vivo gene transfer, 317-318 receptor and uptake, 268 vascular cell gene transfer in vitro, 268-269 adventifial delivery, 272-274, 312-313 balloon angioplasty, hyperplasia prevention with kallikrein gene delivery in rats, 261-262 716 SUBJECT INDEX catheters for delivery, 312 clinical prospects, 319-320 limitations, 311 target cells, 311 e x vivo gene delivery, 313,317-318 Brain adenovirus gene transfer dosing of vector, 294-295 first-generation vectors, 293 gutless vectors advantages, 294-295 cell lines for expression, 309 construction using Flpe recombinase, 305,307-308 helper virus generation, 308 models for study, 297 quality assessment, 304 rescue and amplification from plasmids, 309 titration, 310 transgene expression levels, 297-299 transport on dry ice, 304-305 immune response, 295, 297 immunization against vectors and neutralizing serum antibody assays, 303-304 immunohistochemical analysis antibodies, 301-302 sample preparation, 300-301 promoters, 294 reporter assays of transgene expression fl-galactosidase activity, 300 immunohistochemistry, 300-301 quantitative analysis, 302 real-time reverse transcriptase-polymerase chain reaction, 302-303 stereotactic surgery in rats, 299-300, 310 toxicity of vectors, 293-294 feline immunodeficiency virus vector gene transfer clinical applications, 433-434, 453 injection into mouse striatum or cerebellum cerebellum, 447-448 materials, 438-439 striatum, 446-447 tissue preparation for immunostaining animal perfusion and fixation, 439, 448-449 brain dissection, 440, 449 dual immunofluorescent staining, 440-441,450-451 fluorescence microscopy, 452-453 materials, 439-441 sectioning, 440, 450 titering approaches, 442 materials, 438 polymerase chain reaction, 443-444 X-Gal staining, 443-444 vector production harvesting, 442 materials, 436-437 transfection, 44 1-442 vesicular stomatitis virus glycoprotein pseudotyping, 435-436, 444-446 stroke, s e e Ischemia-induced neuronal death C CD34 + cells, foamy virus transduction, 645~46 CYP2B 1, pancreas cancer treatment with microencapsulated cell expression, 604-605, 609 Cystic fibrosis feline immunodeficiency virus for airway epithelia transduction gene transfer airway epithelia in vitro, 508-509 end points for assessment, 510, 512 rabbit lower airway, 509-510 rabbit tracheal epithelia, 509 histochemical analysis fixation, 512 nuclear fast red counterstaining, 514 paraffin embedding of tissue, 513 X-Gal staining, 512-513 model systems animal models, 505-506 bronchial xenografts, 506 epithelia culture, 503-504 factors in selection, 502-503 immortalized cell lines, 503 tracheal explant, 504-505 rationale, 501-502 vector production formulation, 507-508 plasmids, 506-507 transfection, 507 SUBJECT INDEX gene mutations, 500 gene therapy prospects, 500-501, 512 D Dendrimer, organ transplantation gene transfer, 203 DNA vaccine advantages, 107 aurintricarboxylic acid effects on efficacy, 76-77, 90 discovery of transgene expression, 72-73 efficiency, 90 electroporation for in vivo gene transfer, 80, 88 heart gene transfer in mouse anesthesia, 135-136 applications, 134-135 DNA preparation, 136 duration of expression, 134 efficiency, 134 reporter genes assays, 141-142 selection, 141 surgery, 136-139 tissue harvesting and homogenization, 140-141 variability sources and minimization, 139-140 intestine gene transfer in mouse, 132 intravascular injection of plasmid DNA for gene transfer in mouse liver comparison of sites, 128 intra-bile duct injection, 127 intraportal injection, 126 intra-vena cava, 126-127 overview, 125 tail vein injection, 127-128 kidney gene transfer in mouse, 132 muscle injection monkey, 130-131 rat, 129-130 organ transplantation gene transfer, 202 ovary gene transfer in rat, 133 testis gene transfer in rat, 133 E EBV vectors, see Epstein-Burr virus vectors EIAV, see Equine infectious anemia virus 717 Electroporation, in vivo gene transfer dielectric insulating material for tissue current reduction charge-shielding effects, 82-84 electrical properties of tissues, 81-82 films, 83-85 rationale, 81 mouse studies of gene transfer enhancement animals, 85 dielectric insulating material-coated electrode testing, 89 humoral response analysis, 88-89 intraderrnal DNA injection and electroporation, 88 luciferase assay, 86-87 muscle electroporation, 88 plasmid preparation, 86 muscle, 78, 80 optimization parameters, 78 prospects, 91 rationale, 77 skin, 80 technique, 77-78 toxicity, 90-91 Embryonic stem cell, organ transplantation gene transfer endocrine cell differentiation, 214 gene transduction, 216-217 transplantation of single cells materials, 217-218 portal vein injection, 218 renal subcapsular injection, 218 Epstein-Burr virus vectors application potential for gene therapy, 651-652, 659-660 genome features, 649-650 human artificial episomal chromosome system, 649-650 miniEBV vectors functional complementation assay in human disease cells, 656-658 helper cell and virus, 660 Northern blot analysis of transgene expression, 657 overview, 650-652 preparation, 652 suicide strategy for B lymphoma gene therapy, 658-659 titering, 653 transduction 718 SUBJECT INDEX cells from human disease, 653 chromosomal association of episomal DNA, 655-656 episomal maintenance in stably transduced cells, ~ transfection, 652 tropism, 651-652, 660 Equine infectious anemia virus applications, 491-493 genome structure and function dUTPase, 469-470 long terminal repeat, 468 Rev, 468-469 $2, 469 size, 467 Tat, 468 host range, 466-467 minimal vector system central polypurine tract modification, 476 design, 470 Gag/Pol gene, 473-474 genome structure, 470-471 pseudotyping of envelope, 474-475 Rev/RRE influence on titer, 471 size capacity, 471,473 woodchuck hepatitis posttranscriptionai regulatory element utilization, 476 prospects for gene therapy, 493-494 replication-competent retrovirus assays for vectors cell line selection for amplification, 487-489 establishment, 489-490 federal regulatory requirements, 489 producer cells, 491 recombination and competent virus formation, 485-486 safety profile of vectors, 483-485 supernatant assays, 490 test system relevance, 487 validation, 489 titering with polymerase chain reaction for unmarked genomes DNA preparation from transduced cells, 495-496 product enhanced reverse transcriptase assay, 481,483, 498-499 Taqman real-time assay for vector RNA, 478-480, 496-498 vector production harvesting and concentrating, 494-495 stable producer systems, 477-478 transient production, 477 Erythropoietin adeno-associated virus dual vector heterodimerization vector, 341 helper-dependent adenoviral vector delivery, 195 F Factor VIII, expression and quantification from retroviral vectors, 576, 583, 585-587 Fas ligand apoptosis induction with adenoviral vector green fluorescent protein fusion protein expression cell culture, 541-542 design of vector, 533-537 infectious particle titration, 543-544 large-scale production of vector, 544-545 ligation assembly of genome and transfection, 532-533, 538-542 lysate preparation, 542-543 packaging cell line development expressing CrmA and Bcl2, 537-538 wild-type revertant detection, 546-547 organ transplantation gene transfer, 205-206 Feline immunodeficiency virus vectors airway epithelia transduction gene transfer airway epithelia in vitro, 508-509 end points for assessment, 510, 512 rabbit lower airway, 509-510 rabbit tracheal epithelia, 509 histochemical analysis fixation, 512 nuclear fast red counterstaining, 514 paraffin embedding of tissue, 513 X-Gal staining, 512-513 model systems animal models, 505-506 bronchial xenografts, 506 epithelia culture, 503-504 factors in selection, 502-503 immortalized cell lines, 503 tracheal explant, 504-505 rationale, 501-502 vector production formulation, 507-508 SUBJECT INDEX plasmids, 506-507 transfection, 507 brain gene transfer clinical applications, 433-434, 453 injection into mouse striatum or cerebellum cerebellum, 447-448 materials, 438-439 striatum, 446-447 tissue preparation for immunostaining animal perfusion and fixation, 439, 448-449 brain dissection, 440, 449 dual immunofluorescent staining, 440-44 1,450-451 fluorescence microscopy, 452-453 materials, 439-441 sectioning, 440, 450 titering approaches, 442 materials, 438 polymerase chain reaction, 443-444 X-Gal staining, 443-444 vector production harvesting, 442 materials, 436-437 transfection, 44 1-442 vesicular stomatitis virus glycoprotein pseudotyping, 435-436, 444-446 genome, 435 replication, 435 Feline leukemia virus, pseudotyping, 475-476 FIV vectors, s e e Feline immunodeficiency virus vectors Foamy virus genome and genes, 629, 631 host range, 631 infection cell cycle requrements, 631-633 effects, 628-629 production and titration for replicationcompetent retrovirus assay, 640-641 vectors concentrating with ultracentrifugation, 638-639 deleted vectors, 636-637 helper assay with foamy marker rescue, 639-640 helper virus testing, 635-636 FV, 719 history of production, 633 packaging cells, 633-634 prospects, 648 safety, 628-629 size capacity, 647 stock freezing and thawing, 639 Tas-independent production, 634-635, 637-638 transduction adherent cells with alkaline phosphatase vectors, 641-642 CD34 + ceils from humans, 645-646 hematopoietic stem cells from mice, 642-645, 647-648 transfection, 637-638 s e e Foamy virus G GALV, s e e Gibbon ape leukemia virus Gene therapy barriers, 72 definition, 311,603 direct versus indirect transfer, 92-93 electroporation, s e e Electroporation, in v i v o gene transfer hydrodynamics-based transfection, s e e Hydrodynamics-based transfection hypertension, s e e Hypertension microencapsulation of cells, s e e Microencapsulation, cells for gene therapy nuclease inhibitor enhancement of delivery, s e e Aurintricarboxylic acid organ targeting, s e e s p e c i f i c o r g a n s phage display for targeting, s e e Phage display regulable gene switches, s e e GLp65; GLVP targeted therapy importance, 157-158 transfection steps, 106 transplantation, s e e Transplantation, gene therapy vectors, s e e s p e c i f i c v e c t o r s GH, s e e Growth hormone Gibbon ape leukemia virus, pseudotyping, 475, 575,580 GLp65 adenovirus vector utilization, 555, 559-560 clinical prospects, 561 development, 554-555 intramuscular injection, 558-559 720 SUBJECT L~rDEX mifepristone regulation, 551,555, 559 production design, 555,557 transfection, 558 GLVP characterization in cell culture and transgenic mice, 552-554, 559-561 humanized gene switch, s e e GLp65 mifepristone regulation, 551,553-554 production design, 555, 557 transfection, 558 progesterone receptor engineering, 551-552 Growth hormone GLp65 utilization for adenoviral delivery, 555, 559-560 helper-dependent adenoviral vector delivery, 194 H Hairpin ribozyme autosomal dominant retinitis pigmentosa, ribozyme gene therapy adeno-associated virus vector packaging, 376-377 cloning of ribozymes and targets adeno-associated virus vector DNA purification, 366-368 oligonucleotide purification and phosphorylation, 366 overview, 365 materials, 362-363 rationale, 361-362 ribozyme design, 364-365 target site identification, 363 structure and function, 359-360 Hammerhead ribozyme autosomal dominant retinitis pigmentosa, ribozyme gene therapy adeno-associated virus vector packaging, 376-377 cleavage assay long RNA targe transcription and cleavage time courses, 373-375 multiple turnover kinetic analysis, 370-373 RNA deprotection and phosphorylation, 368-369 time course analysis, 369-370 cloning of ribozymes and targets adeno-associated virus vector DNA purification, 366-368 oligonucleotide purification and phosphorylation, 366 overview, 365 materials, 362-363 rationale, 361-362 ribozyme design, 363-364 target site identification, 363 structure, 359 substrate specificity, 360-361 Heart, gene transfer, s e e a l s o Blood vessel, gene transfer application prospects, 323 excitability manipulation with adenoviral vectors animal models, 333-334 cell isolation, 326 confocal imaging of ion channel transgenes, 327-328 intramyocardial injection, 323-326 intravascular delivery catheterization models and efficiency, 328-329 efficiency parameters, 329-330 microvascular permeability factors for increasing delivery, 330-332 vector constructs, 324 intracoronary infusion gene transfer in mouse, 223-224 intravascular gene transfer in mouse anesthesia, 135-136 applications, 134-135 DNA preparation, 136 duration of expression, 134 efficiency, 134 reporter genes assays, 141-142 selection, 141 surgery, 136-139 tissue harvesting and homogenization, 140-141 variability sources and minimization, 139-140 kallikrein delivery in rats with adenovirus vector adenovirus preparation, 247-249 apoptosis assay, 256-257 blood pressure response, 259-260 SUBJECT INDEX blood vessel hyperplasia inhibition after balloon angioplasty, 261-262 cardiac function assay with fluorescent microspheres, 255-256 cardiomyocyte diameter response, 250-253 cardiovascular benefits, 260-261,263 expression level and time course, 259 rationale, 247 superoxide histochemistry, 257-258 tissue distribution of transgene, 258-259 vector delivery routes carotid artery, 249 intracerebroventricular, 250 intramuscular, 249 intra-salivary gland, 250 intravenous injection, 249 Hemagglutinating virus of Japan-liposomes gene transfer advantages, 619 cells, 626-627 mechanism, 619 in v i v o , 627 lipid composition, 622 oligodeoxynucleotide uptake by cells, 621 preparation conjugates, 623-624, 626 lipid mixtures, 623,625-626 materials, 623-624 virus preparation chorioallantoic fluid preparation, 624-625 egg preparation, 624-625 materials, 623 repeated injection, 620 Hematopoietic stem cell, foamy virus transduction, 642-645,647-648 Herpes simplex virus amplicon vectors advantages, 593 gene transfer conditions, 601 helper virus-free packaging system, 594-595 production cosmid amplification, 596 cosmid preparation, 598-599 DNA purification, 596-598 tissue culture, 599 titering, 600-601 transfection, 599-600 virus harvesting and concentration, 600 721 prospects, 601-603 size capacity, 593 organ transplantation gene transfer, 201 HIF- l ot, s e e Hypoxia-inducible factor-let HIV vectors, s e e Human immunodeficiency virus vectors HSC, s e e Hematopoietic stem cell HSV, s e e Herpes simplex virus Human immunodeficiency virus vectors first-generation vectors, 455 infectivity enhancement, 457-458 large-scale production and concentration, 569-571 pseudotyping, 445 safety, 455, 457 self-inactivating vectors, 457 stable packaging cell lines, 457 third-generation, replication-defective, pseudotyped vectors bulk assays of transducing activity copy number of vector integration per genome, 523-524 maximal transduction frequency, 522-523 end-point titration of vector transducing activity, 520-522 genome features, 515 infectivity calculation from vector stock, 524-526 production in third-generation packaging system concentrating, 462 p24 assay, 463 plasmids, 459, 515 replication competence testing, 464-465 RNA slot-blot assay, 464 transfection, 459, 461 quality control p24 assay, 519-520 reverse transcriptase assay, 519-520 RNA assay, 519-520 transducing activity assay, 518-519 safety, 515-516 self-inactivating transfer vector, 516 transduction cell culture, 526-527 pseudotransduction effects, 527-528 vector concentration, 527 transfer vector construction, 516-518 tropism, 454 722 SUBJECT INDEX Hydrodynamics-based transfection blood vessels in transfection, 94 injection of mice, 94-95 luciferase assay, 95-96 optimization injection volume, 96-97 speed of injection, 97 toxicity evaluation, 97-99 plasmid preparation, 94 principles, 93-94 transgene expression efficiency, 99-101 persistence, 101,103-104 repeated administration effects, 104-105 Hypertension angiotensin II type receptor, antisense delivery with Moloney murine leukemia virus delivery to neonatal rats, 567 hypertension effects in spontaneously hypertensive rat, 563,567-569 large-scale production of virus, 566-567 packaging cell production, 563-565 titering of vector encoding drug resistance marker, 565-566 gene therapy adeno-associated virus vectors, 9-11, 13 adenovirus vectors, 11 overview of approaches, 3-4 retrovirus vectors, 12 vasoconstrictor gene antisense /~l-adrenoreceptor antisense, angiotensinogen antisense, angiotensin receptor type antisense, 8-9 antisense oligodeoxynucleotide delivery, 5-6, 12 overview of targets, 5, 13 viral vectors, vasodilation gene therapy, 4-5, 13 kallikrein delivery in rats with adenovirus adenovirus preparation, 247-249 blood pressure response, 259-260 cardiac function assay with fluorescent microspheres, 255-256 cardiovascular benefits, 260-261,263 rationale, 247 regional blood flow response, 254-255 renal hemodynamic effects, 253,261 pharmacotherapy, treatment barriers, 3, 13 Hypoxia-inducible factor-lu, angiogenesis gene therapy, 146-147 I IL- 10, see Interleukin- 10 Interleukin-10, organ transplantation gene transfer, 204 Intestine, intravascular gene transfer in mouse, 132 Ischemia-induced neuronal death bcl-2 delivery for ischemia-induced neuronal death with adeno-associated virus vector epitope tagging of transgene, 379-381 gerbil model hippocampal apoptosis assay, 391 histochemical analysis of epitope-tagged Bcl-2, 388-389, 391 injection of vector in brain, 387-388 ischemia induction, 384-385 rationale, 378-379 vector production with triple plasmid transfection materials, 382-383 principles, 381-382 purification, 384 transfection, 383 stroke mechanisms, 378 K Kallikrein, adenovirus delivery in rats adenovirus preparation, 247-249 apoptosis assay, 256-257 blood pressure response, 259-260 blood vessel hyperplasia inhibition after balloon angioplasty, 261-262 cardiac function assay with fluorescent microspheres, 255-256 cardiomyocyte diameter response, 250-253 cardiovascular benefits, 260-261,263 expression level and time course, 259 rationale, 247 regional blood flow response, 254-255 renal hemodynamic effects, 253, 261 superoxide histochemistry, 257-258 tissue distribution of transgene, 258-259 vector delivery routes SUBJECT INDEX carotid artery, 249 intracerebroventricular, 250 intramuscular, 249 intra-salivary gland, 250 intravenous injection, 249 Kidney intravascular gene transfer in mouse, 132 kallikrein delivery in rats with adenovirus vector adenovirus preparation, 247-249 glomerular filtration rate measurement, 253-254, 261 rationale, 247 renal blood flow measurement, 253-254, 261 vector delivery routes carotid artery, 249 intracerebroventricular, 250 intramuscular, 249 intra-salivary gland, 250 intravenous injection, 249 L Lentivirus advantages for neuronal gene transfer, 434-435 gene discovery and target validation use of vectors, 493 genomes, 454-455 hypertension gene therapy vectors, 12 organ transplantation gene transfer, 201 production of vectors cell culture and transfection, 583 design, 583-584 harvesting, 584 overview, 576-579 pseudotyping, 579, 587 titration, 584, 589 yields of transgene, 587-588 targets of vectors brain, 491-492 hematopoietic stem cells, 492 liver, 492 muscle, 492-493 overview, 491, 514 types of vectors, 458-459, 563 vectors, s e e Equine infectious anemia virus; Feline immunodeficiency virus vectors; Human immunodeficiency virus vectors 723 vesicular stomatitis virus glycoprotein pseudotyping of vectors, 435-436, 444-446, 454, 474, 514 Leptin, helper-dependent adenoviral vector delivery, 194-195 Lipoplex, definition, 107 Liposome hemagglutinating virus of Japan complexes, s e e Hemagglutinating virus of Japan-liposome oligonucleotide-mediated site-directed gene repair, encapsulation of RNA/DNA oligonucleotides encapsulation efficiency determination, 18-20 extrusion, 17-18 liposome preparation, 17 liver targeting, 16, 22-23 phospholipid determination, 18 scale-up, 20-21 size distribution of liposomes, 18 stability testing, 20, 22-23 organ transplantation gene transfer, 202 stabilized plasmid-lipid particles, s e e Stabilized plasmid-lipid particles Liver helper-dependent adenoviral vector expression, 196 hydrodynamics-based transfection, s e e Hydrodynamics-based transfection intravascular injection of plasmid DNA for gene transfer in mouse comparison of sites, 128 intra-bile duct injection, 127 intraportal injection, 126 intra-vena cava, 126-127 overview, 125 tail vein injection, 127-128 oligonucleotide-mediated site-directed gene repair, 16, 22-23 organ transplantation gene transfer, 220, 222-223 M Microencapsulation, cells for gene therapy historical perspective, 603-604 interleukin- 12 delivery, 617 pancreas cancer treatment with microencapsulated cells 724 SUBJECT INDEX angiographic delivery, 612, 614 animal models, 609-611 chemotherapy limitations, 604 clinical trial in humans, 614-616 CYP2B1 expression, 604-605, 609 encapsulation, 606, 609 rationale, 604-605 vector construct, 605 prospects for cancer therapy, 617-618 rationale, 603 vascular delivery, 617-618 Mifepristone-regulated gene switches, s e e GLp65; GLVP MMLV, s e e Moloney murine leukemia virus Moloney murine leukemia virus angiotensin II type receptor antisense delivery delivery to neonatal rats, 567 hypertension effects in spontaneously hypertensive rat, 563, 567-569 large-scale production of virus, 566-567 packaging cell production, 563-565 titering of vector encoding drug resistance marker, 565-566 organ transplantation gene transfer, 200 pseudotyping, 475, 575-576 Muscle, s e e a l s o Myoblast-mediated gene transfer DNA injection monkey, 130-131 rat, 129-130 heart intravascular gene transfer in mouse anesthesia, 135-136 applications, 134-135 DNA preparation, 136 duration of expression, 134 efficiency, 134 reporter genes assays, 141-142 selection, 141 surgery, 136-139 tissue harvesting and homogenization, 140-141 variability sources and minimization, 139-140 Myoblast-mediated gene transfer advantages, 149-150 angiogenesis therapy controlled angiogenesis approach, 146-148 growth factors, 145-146 histochemical assessment, 154 vascular continuity assessment with fluorescent microbead perfusion, 154-157 myoblast implantation into skeletal muscle, 152-154 myoblast isolation and primary culture from mouse, 150-151 principles, 148-149 retroviral infection of primary myoblasts, 151-152 N NLS, s e e Nuclear localization signal Nuclear localization signal, peptide nucleic acid hybrids for gene delivery oligonucleotide hybridization, 119 oligonucleotide shift analysis, 118 plasmid preparation and hybridization, t 18, 122 plasmid shift analysis, 118 subcellular localization of fluorophore-labeled oligonucleotide complexes, 117 synthesis, 116-117 transfection cell lines, 122 oligonucleotide complexes, 120-121 plasmid complexes, 119-120 Nucleic acid vaccine, s e e DNA vaccine O Oligonucleotide-mediated site-directed gene repair applications, 14-15 chimeric RNA/DNA oligonucleotide design, 14 liposome encapsulation of RNA/DNA oligonucleotides encapsulation efficiency determination, 18 -20 extrusion, 17-18 liposome preparation, 17 liver targeting, 16, 22-23 phospholipid determination, 18 scale-up, 20-21 size distribution of liposomes, 18 stability testing, 20, 22-23 SUBJECT INDEX polyethyleneimine delivery of RNA/DNA oligonucleotides charge of complexes, 28 lactosylation for liver targeting, 24-27 primary amine assay, 26-27 rationale, 24 receptor specificity of uptake, 28 size determination of complexes, 27 stability of complexes, 28 transfection efficiency, 28 site-directed repair detection DNA isolation and subcloning, 30-31 filter lift hybridization assay, 31-33 restriction fragment length polymorphism detection, 33, 35 Ovary, intravascular gene transfer in rat, 133 P Pancreas cancer treatment with microencapsulated cells angiographic delivery, 612, 614 animal models, 609-611 chemotherapy limitations, 604 clinical trial in humans, 614-616 CYP2B expression, 604-605, 609 encapsulation, 606, 609 rationale, 604-605 vector construct, 605 islets, organ transplantation gene transfer gene transduction, 217 isolation, 215-216 transplantation of single cells materials, 217-218 portal vein injection, 218 renal subcapsular injection, 218 P C R , s e e Polymerase chain reaction PDGF, s e e Platelet-derived growth factor PEI, s e e Polyethyleneimine Peptide nucleic acid Bioplex definition, 107 principles, 107-108 prospects, 124 functional hybrid construction, 111-112 melting temperature for DNA complexes, 111 nuclear localization signal hybrids oligonucleotide hybridization, 119 oligonucleotide shift analysis, 118 725 plasmid preparation and hybridization, 118, 122 plasmid shift analysis, 118 subcellular localization of fluorophore-labeled oligonucleotide complexes, 117 synthesis, 116-117 transfection cell lines, 122 oligonucleotide complexes, 120-121 plasmid complexes, 119-120 nucleic acid delivery criteria adhesion to cells, 115 endocytic vesicle avoidance and escape, 116 membrane penetration, 116 nuclear entry, 113 overview, 112-113 packaging of nucleic acid, 113-115 rationale for gene transfer utilization, 108-109 structure of DNA complexes, 108-109 Phage display applications, 163 gene delivery targeting application of peptides biopanning against ectopically expressed receptors, 174-176 biopanning on nontarget cells, 171-172 biopanning on target cell cultures, 169-171 DNA isolation and sequencing, 172-173 materials, 167-168 overview, t64-166 phage amplification, 171 phage purification, 171 phage specificity characterization, 173-174 titration of libraries, 168-169 length of displayed peptides, 167 linear versus constrained libraries, 166-167 principles, 161,163 Platelet-derived growth factor, angiogenesis gene therapy, 145-146 PNA, s e e Peptide nucleic acid Polyethyleneimine, oligonucleotide-mediated site-directed gene repair, RNA/DNA oligonucleotide delivery charge of complexes, 28 lactosylation for liver targeting, 24-27 primary amine assay, 26-27 rationale, 24 726 SUBJECT INDEX receptor specificity of uptake, 28 size determination of complexes, 27 stability of complexes, 28 transfection efficiency, 28 Polymerase chain reaction adeno-associated virus recombinant vector titering, 423-424 equine infectious anemia virus vector titering DNA preparation from transduced cells, 495-496 product enhanced reverse transcriptase assay, 481,483,498-499 replication-competent retrovirus assays, 490 Taqman real-time assay for vector RNA, 478-480, 496-498 feline immunodeficiency virus vector titering, 443-444 RNA assays, s e e Reverse transcriptase-polymerase chain reaction Polyplex, definition, 107 R Restriction fragment length polymorphism, oligonucleotide-mediated site-directed gene repair detection, 33, 35 Retrovirus, s e e a l s o Foamy virus; Lentivirus; Moloney murine leukemia virus advantages in gene therapy, 562 hypertension gene therapy vectors, 12 myoblast-mediated gene transfer, 151-152 oncoretrovirus limitations in gene therapy, 562, 589 production of oncoretroviral vectors cell lines and culture, 579-580 factor VIII expression and quantification, 576, 583,585-587 harvesting, 581 overview, 573-576 pseudotyping, 575-576, 580-581, 585-586, 589 Southern blot analysis, 581 titration, 581-582 prospects for gene therapy, 571-573 Reverse transcriptase-polymerase chain reaction /%galactosidase reporter detection in blood vessels, 319 real-time detection of brain transgene expression, 302-303 RFLP, s e e Restriction fragment length polymorphism Ribozyme, s e e a l s o Hairpin ribozyme; Hammerhead ribozyme autosomal dominant retinitis pigmentosa, ribozyme gene therapy adeno-associated virus vector packaging, 376-377 cleavage assay for hammerhead ribozyme long RNA targe transcription and cleavage time courses, 373-375 multiple turnover kinetic analysis, 370-373 RNA deprotection and phosphorylation, 368-369 time course analysis, 369-370 cloning of ribozymes and targets adeno-associated virus vector DNA purification, 366-368 oligonucleotide purification and phosphorylation, 366 overview, 365 materials, 362-363 rationale, 361-362 ribozyme design hairpin ribozyme, 364-365 hammerhead ribozyme, 363-364 target site identification, 363 classification, 358 gene therapy utilization, 358-359, 361 organ transplantation gene transfer, 206 reaction types, 358 RT-PCR, s e e Reverse transcriptase-polymerase chain reaction RU486, s e e Mifepristone-regulated gene switches S Sendai virus, s e e Hemagglutinating virus of Japan-liposomes SPLP, s e e Stabilized plasmid-lipid particles Stabilized plasmid-lipid particles cationic lipids content variation, 47, 49-51 post-insertion of polyethylene glycol lipids, 52-53 types, 51-52 circulation lifetime, ~ cryoelectron microscopy, 43-44, 46 SUBJECT INDEX density centrifugation for isolation, 42 detergent dialysis for encapsulation, 37-38, 40-42 dosing, 64-65 encapsulation efficiency of various techniques, 65-67 formulation concentration by Amicon, 70 free DNA remocal, 70 lipid preparation, 68-69 materials, 68 salt curve analysis, 69-70 sterilization and storage, 71 sucrose density centrifugation, 71 gene expression following intravenous injection, 62-64 nuclease protection assays, 46-47 polyethylene glycol coating, 37-38, 40, 64 rationale for development, 36-37 size distribution determination, 42 stability testing, 47, 65 stoichiometry of complexes, 43 transfection, in vitro, 53, 55-58 tumor accumulation, 60-6 Stroke, s e e Ischemia-induced neuronal death T Testis, intravascular gene transfer in rat, 133 TGF-/3, s e e Transforming growth factor-/~ Transforming growth factor-/3, organ transplantation gene transfer, 204 Transplantation, gene therapy applications, 199 cellular transplant vector administration embryonic stem cells endocrine cell differentiation, 214 gene transduction, 216-217 overview, 214 pancreatic islets gene transduction, 217 isolation, 215-216 transplantation of single cells materials, 217-218 portal vein injection, 218 renal subcapsular injection, 218 immune response adenovirus vectors, 213 alloantigen-specific adaptive immunity, 213-214 727 graft rejection, 211 innate immunity, 211-212 parenchymal organ transplants, vector administration donor treatment, 219-220 liver gene transfer with adenoviral injection of donor, 220 overview, 218-219 recipient treatment, 219 e x vivo gene delivery to whole organs adenovirus transfer in rat liver, 222-223 heart intracoronary infusion gene transfer in mouse, 223-224 overview, 221-222 promoter selection chimeric and synthetic promoter elements, 208-209 regulatable promoters, 209-210 targeted promoters, 207-208 viral promoters, 206-207 transgenes Fas ligand, 205-206 interleukin- 10, 204 leukocyte adhesion inhibitors, 204-205 major histocompatibility complex genes, 205 ribozymes, 206 selection criteria, 203 T cell costimulation blockers, 205 transforming growth factor-/~, 204 types, 203-204 xenoanigen inhibitors, 206 vectors adeno-associated virus, 201 adenovirus, 201 cationic liposomes, 202 dendrimers, 203 herpes simplex virus, 201 hybrid viral vectors, 201-202 lentivirus, 201 Moloney murine leukemia virus, 200 naked DNA, 202 selection criteria, 199 V Vascular endothelial growth factor angiogenesis gene therapy, 145-146, 148, 154-155 728 SUBJECT INDEX microvascular permeability factor for increasing lentiviral vectors, 435-436, 444-446, 454, adenoviral transgene delivery, 332, 334 474, 514 targeting of gene therapy, 165 oncoretrovirus vectors, 575-576, VEGF, s e e Vascular endothelial growth factor 580-581 Vesicular stomatitis virus glycoprotein, VSV-G, s e e Vesicular stomatitis virus glycoprotein pseudotyping ISBN 0-12-182247-8 J[!rli°°ifr !fLrllK lllJJ 822477 ... this is the first volume entitled "Gene Therapy Methods" for the Methods in Enzymology series, the increasing number of new methods and the progress of gene therapy will undoubtedly require more... hypertension is a multigene disease, how can we decide on the candidate genes for gene therapy? We have ignored the difficulties of defining all the candidate genes by concentrating on the genes that have... 101, 682 (2000) [ 1] GENE THERAPYFOR HYPERTENSION TABLE III PRECLINICALDATA ON GENE THERAPY FOR HYPERTENSION, VASOCONSTRICTORGENES: VIRAL VECTORDELIVERY OF ANTISENSE Target gene Delivery AGT AAV-based