# Readings

Course readings.
WEEK # | TOPICS | READINGS | READING NOTES
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1 | Introduction See the Lecture Summary | [no readings] |
2 | From Stem Cells to Blood See the Lecture Summary | Paper 2a: Identification of a factor that determines if donor HSCs are compatible with the recipient. Bach, F. H., and D. B. Amos. "Hu-1: Major Histocompatibility Locus in Man." Science 156 (1967): 1506-1508. | It had recently been shown that HSCs exist. The question was how to determine if HSCs from one individual would be able to reconstitute the hematopoietic system of another individual. If the procedure failed the recipient would die. How did this paper reduce the risk for patients receiving HSC transplantations?
Paper 2b: HSCs from siblings are used to treat a deadly genetic disorder. Gatti, R. A., H. J. Meuwissen, H. D. Allen, R. Hong, and R. A. Good. "Immunological Reconstitution of Sex-linked Lymphopenic Immunological Deficiency." Lancet 2 (1968): 1366-1369. | This paper is one of the first that demonstrates a clinical application for HSC transplantations. The paper describes the first successful human bone marrow transplant for an illness other than cancer. Why were only boys in this family dying from this disorder? Why was this child cured using HSCs from his sister? What complications could have been expected?
3 | Gene delivery vehicles engineered from viruses See the Lecture Summary | Paper 3a: Discovery of RNA-dependent DNA-polymerase in retrovirus. Temin, H. M., and S. Mizutani. "RNA-dependent DNA Polymerase in Virions of Rous Sarcoma Virus." Nature 226 (1970): 1211-1213. | In 1970 Howard Temin and his postdoctoral student Satoshi Mizutani announced that they had detected a viral enzyme that was able to transcribe single-stranded viral RNA into DNA. Temin and Mitzutani were the first to figure out how retroviruses work. This paper and the accompanying paper by David Baltimore resulted in awarding of the Nobel prize to Temin and Baltimore. How did Temin prove the existence of an RNA dependent DNA polymerase? How did this paper forward the field of gene therapy? Why was the discovery of an RNA dependent DNA polymerase important for the whole field of molecular biology?
Paper 3b: A method to deliver genes for gene therapy using modified human immunodeficiency virus. Naldini, L., U. Blomer, P. Gallay, D. Ory, R. Mulligan, F. H. Gage, I. M. Verma, and D. Trono. "In vivo Gene Delivery and Stable Transduction of Nondividing Cells by a Lentiviral Vector." Science 272 (1996): 263-267. | Twenty six years after the previous paper was published much more was known about retroviruses. Research involving the lentivirus HIV had been intense, and the knowledge led to unexpected uses of the virus. This paper describes the production of "safe" lentiviral vectors that can be used for gene therapy. The last author Didier Trono, is now the Dean of Life Sciences at the Swiss equivalent of MIT. What are the risks of using retroviral vectors based on HIV for gene transfer into human cells? How did these authors get around some of these risks? How can a virus particle be engineered to target specific cell types?
4 | Treating genetic disorders by fixing the bad gene. See the Lecture Summary | Paper 4a: The first successful gene therapy trial. Cavazzana-Calvo, M., et al. "Gene Therapy of Human Severe Combined Immunodeficiency (SCID)-X1 Disease." Science 288 (2000): 669-672. | The first successful gene therapy trials described in this paper were both a huge success and a failure for the field of gene therapy. For the first time it was possible to genetically correct HSCs from patients with X-SCID. Why was this trial conducted on X-SCID patients and not on patients with another monogenetic disorder? Was the chance of success higher in this group or was the risk-benefit ration particularly high? How can we know that the genetic defect was corrected in HSCs of cells transplanted to these children?
Paper 4b: Leukemia develops in patients treated with gene therapy. Hacein-Bey-Abina, S., C. Von Kalle, M. Schmidt, M. P. McCormack, N. Wulffraat, P. Leboulch, A. Lim, C. S. Osborne, R. Pawliuk, E. Morillon, R. Sorensen, A. Forster, P. Fraser, J. Cohen, G. de Saint Basile, I. Alexander, U. Wintergerst, T. Frebourg, A. Aurias, D. Stoppa-Lyonnet, S. Romana, I. Radford-Weiss, F. Gross, F. Valensi, E. Delabesse, E. Macintyre, F. Sigaux, J. Soulier, L. Leiva, M. Wissler, C. Prinz, T. H. Rabbitts, F. Le Deist, A. Fischer, and M. Cavazzana-calvo. "LMO2-associated Clonal T Cell Proliferation in Two Patients After Gene Therapy for SCID-X1." Science 302 (2003): 415-419. | Two years later this paper appeared. The bad news is that 2 out of 9 patients from the X-SCID study had developed T cell leukemia. Was this a result of gene therapy? Why did the patients get similar forms of T-cell leukemia? Would you have stopped the clinical trial based on the risk of developing leukemia? What are the options for these children?
5 | RNAi: Using an ancient defense against viral infection to turn off disease genes See the Lecture Summary | Paper 5a: Discovery of RNA interference, a mechanism and tool for specific down regulation of gene expression. Fire, A., S. Xu, M. K. Montgomery, S. A. Kostas, S. E. Driver, and C. C. Mello. "Potent and Specific Genetic Interference by Double-stranded RNA in Caenorhabditis Elegans." Nature 391 (1998): 806-811. | In 1998 Fire and Mello published this groundbreaking study in which they found to their surprise that double-stranded RNA caused a potent and specific gene silencing while single-stranded antisense RNA had only a modest effect. Why was this discovery so important? Is it possible that this evolutionarily conserved mechanism of silencing gene expression from double stranded RNAs was developed as a protection against pathogens?
Paper 5b: Development of a method to deliver and regulate RNA interference to cells using lentiviral vectors. Wiznerowicz, M., and D. Trono. "Conditional Suppression of Cellular Genes: Lentivirus Vector-mediated Drug-inducible RNA Interference." J Virol 77 (2003): 8957-8961. | This paper describes lentiviral vectors that mediate down-regulation of specific genes in target cells. How was the gene-silencing effect of RNA interference delivered to cells? How can you turn this silencing on and off? Where does the tetracycline-resistance operon (tetO) come from? What are possible applications of this method?
6 | Future of personalized medicine using induced pluripotent stem (iPS) cells See the Lecture Summary | Paper 6a: Reprogramming fibroblasts to pluripotent stem cells that are similar to embryonic stem cells. Takahashi, K., and Yamanaka, S. "Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors." Cell 126 (2006): 663-676. | This is one of the most important scientific publications in recent years. What are the differences among HSCs, embryonic stem (ES) cells and iPS cells? Why is this paper important in the context of ethical considerations of stem cell research?
Paper 6b: Proof of principle that reprogramming of fibroblasts may be used for cell therapy of genetic hematological disorders. Hanna, J., M. Wernig, S. Markoulaki, C. W. Sun, A. Meissner, J. P. Cassady, C. Beard, T. Brambrink, L. C. Wu, T. M. Townes, and R. Jaenisch. "Treatment of Sickle Cell Anemia Mouse Model with iPS Cells Generated from Autologous Skin." Science 318 (2007): 1920-1923. | Here the potential of iPS cells as treatment for genetic disorders is demonstrated. What is a "humanized sickle cell mouse"? How is the genetic defect corrected? How are iPS cells converted into HSCs? What are the obstacles to overcome before this approach can be used in the clinic?
7 | Field trip to the Whitehead Institute and to the Whitehhead Flow Cytometry Facility See the Lecture Summary | [no readings] |
Week 8 - Week 13: The journey of a 'wonder' drug, Gleevec
8 | Identification of bcr-abl translocation and its oncogenic properties See the Lecture Summary | Paper 8a: The molecular identification of bcr-abl in chronic myeloid leukemia. Heisterkamp, N., J. Stephenson, J. Groffen, P. Hansen, A. Klein, C. Bartram, and G. Grosveld. "Localization of the c-abl Oncogene Adjacent to a Translocation Break Point in Chronic Myelocytic Leukemia." Nature 306 (1983): 239-242.
Paper 8b: One of the first studies to show that bcr-abl is the cause of chronic myeloid leukemia in mice. Daley, G., R. Van Etten, and D. Baltimore. "Induction of Chronic Myelogenous Leukemia in Mice by the P210bcr/abl Gene of the Philadelphia Chromosome." Science 247 (1990): 824-830.
9 | Drug development for inhibiting kinase activity in the bcr-abl fusion See the Lecture Summary | Paper 9a: Reported the catalytic tyrosine kinase activity in the bcr-abl fusion. Lugo, T., A. M. Pendergast, A. Muller, and O. Witte. "Tyrosine Kinase Activity and Transformation Potency of bcr-abl Oncogene Products." Science 122 (1990): 1079-1082.
Paper 9b: Documented the rationale for the modifications made in lead compound to be an effective drug. Zimmermann, J., E. Buchdunger, H. Mett, T. Meyer, N. Lydon, and P. Traxler. "Potent and Selective Inhibitors of the ABL-kinase: Phenylaminopyrimidine (PAP) Derivatives." Bioorg Med Chem Lett 7 (1997): 187-192.
10 | Testing the efficacy of Gleevec in cell lines, mouse and human See the Lecture Summary | Paper 10a: Pioneering study that establish the powerful efficacy of Gleevec in bcr-abl-positive leukaemias in vitro and mouse model. Druker, B. J., S. Tamura, E. Buchdunger, S. Ohno, G. Segal, S. Fanning, J. Zimmermann, and N. Lydon. "Effects of a Selective Inhibitor of the Abl Tyrosine Kinase on the Growth of Bcr-Abl Positive Cells." Nature Med 2 (1996): 561-566.
Paper 10b: The first human clinical trial treating CML with Gleevec, documenting a high level of efficacy, minimal level of toxicity and describing the dose-response relationship. Druker, B. J., C. L. Sawyers, H. Hantarjin, D. J. Resta, S. F. Reese, J. M. Ford, R. Capedeville, and M. Talpaz. "Activity of a Specific Inhibitor of the BCR-ABL Tyrosine Kinase in the Blast Crisis of Chronic Myeloid Leukemia and Acute Lymphoblastic Leukemia with the Philadelphia Chromosome." N Engl J Med 344 (2001): 1038-1042.
11 | Evolving resistance to Gleevec See the Lecture Summary | Paper 11a: A detailed and informative description of the structural interactions between Gleevec and the ABL protein using crystallographic studies, which provide significant insight into potential mechanisms of resistance. Schindler., T., W. Bornmann, P. Pellicena, W. Miller, B. Clarkson, and J. Kuriyan. "Structural Mechanism for STI-571 Inhibition of Abelson Tyrosine Kinase." Science 289 (2000): 1938-1942. (PDF - 1.3MB)
Paper 11b: This study describes potential mechanisms of resistance in CML in patients bearing bcr-abl translocation. Gorre, M., M. Mohammed, K. Ellwood, M. Hsu, R. Paquette, P. Rao, and C. Sawyers. "Clinical Resistance to STI-571 Cancer Therapy Caused by bcr-abl Gene Mutation or Amplification." Science 293 (2001): 876-880. (PDF)
12 | Overcoming Gleevec resistance See the Lecture Summary | Paper 12a: The first report to illustrate design and implementation of chemical screen to overcome Gleevec resistance. Shah, N., C. Tran, F. Lee, P. Chen, D. Norris, and C. Sawyers. "Overriding Imatinib Resistance with a Novel ABL Kinase Inhibitor." Science 305, no. 5682 (2004): 399-401.
Paper 12b: Clinical efficacy of, a novel bcr-abl kinase inhibitor, dasatinib in patients developing resistance to Gleevec. Hochhaus, A., H. Kan, M. Baccarani, J. Lipton, J. Apperley, B. Druker, T. Facon, S. L. Goldberg, F. Cervantes, D. Niederwieser, R. Silver, R. Stone, T. Huges, M. Muller, R. Ezzeddine, A. Countoouriotis, and N. Shah. "Dasatinib Induces Notable Hematologic and Cytogenetic Responses in Chronic-phase Chronic Myeloid Leukemia After Failure of Imatinib Therapy." Blood 109, no. 6 (2007): 2303-9.
13 | Use of Gleevec in other diseases See the Lecture Summary | Paper 13a: This study highlights the importance of receptor for stem-cell factor- c-kit, a receptor kinase signaling in the pathogenesis of gastrointestinal stromal tumors. Hirota, S., K. Isozaki, Y. Moriyama, K. Hashimoto, T. Nishida, S. Ishiguro, K. Kawano, M. Hanada, A. Kurata, M. Takeda, T. Muhammad, Y. Matsuzawa, Y. Kanakura, Y. Shinomura, and Y. Kitamura. "Gain of Function Mutations of c-Kit in Human Gastrointestinal Stromal Tumors." Science 279 (1998): 577-580.
Paper 13b: A proof-of-concept documenting the efficacy of Gleevec in kit-expressing gastrointestinal stromal tumors (GIST). Joensuu, H., P. J. Roberts, M. Sarlomo, D. Tuveson, S. L. Silberman, R. Capdeville, S. Dimitrijevic, B. Druker, and G. Demetri. "Effect of the Tyrosine Kinase Inhibitor STI571 in a Patient with Metastatic Gastrointestinal Stromal Tumor." N Engl J Med 344 (2001): 1052-1056.