Therapeutics
Table 4: Comparison of IVR modalities MODALITY
Small molecule
STRENGTHS
WEAKNESSES
Easy to manufacture and administer Development pathway less straightforward Less specific – off target effects and toxicities
RNA
Easy to manufacture Development straightforward
Problematic delivery: stability and specificity May need carriers to target specific cells
Protein
Development straightforward Very specific (cell type, distribution, and mechanisms)
Relatively high manufacture and distribution cost Inconvenient administration
consists of numerous genes and their products (nodes), and the regulatory relations among them (edges). Although all the cells in the human body share one GRN, the state of the GRN differs sig- nificantly among different cell types. For example, some parts of the GRN are active or lightened up in cells, but are inactive or go dark in hepato- cytes and vice versa. In fact, what distinguishes cells from hepatocytes is their internal state of the GRN. The differences in GRN states are due to dif- ferences in cell environment, the legacy compo- nents from parent cells, and the history of cell lin- eages. The goal of the reprogramming process, then, is to perturb one GRN state into another. One way this can be done is to turn on parts of the GRN while simultaneously shutting down the other parts. Transcription factors are the conven- ient choices for perturbing GRN states because they occupy the top layers of the hierarchical GRN. They are the switches for different GRN states.
Comparing the GRN states of two different types of cells may uncover hundreds of transcrip- tion factors that differ significantly in expression. However, there is a shortcut through this maze. Among all of these nodes exists an active kernel that is highly conserved in the same type of cells among different species7. Since certain nodes of such conservative kernels in the product cells are inactive in the substrate cells, the protein prod- ucts of such nodes are instrumental in the conver- sion process.
Using cues from systems biology and confirma- tion from experimental biology, it is not difficult to identify the reprogramming factors given the sub- strate and the product cells. Here we can only pro-
Drug Discovery World Summer 2011
vide the general principles; a more detailed treat- ment is the subject of another article. One key feature of the active kernel module for a specific cell is that it enters a ‘lock on’ state once the cells’ fate is decided. The ‘lock on’ state is maintained through several positive feedback loops initially and then through epigenetic events in the long term. Therefore, after introducing sev- eral key transcription factor proteins and initiating a new GRN state, the external reprogramming fac- tors are no longer necessary. Even when these external reprogramming factors are withdrawn from the environment, the cells will retain the new fate because the new GRN state is maintained internally and becomes very stable, ie ‘locked on’.
Strategy
Any effective cure towards the difficult diseases should fulfill two requirements. First, we need to identify the mechanism behind cell deficiency and halt this cell-destruction mechanism. Second, we need to find a way to replenish the cells. In certain diseases, cell reprogramming can be used to meet the latter requirement and integrated into a holistic therapeutic strategy. For example, in stroke patients, blood clots are cleared and the rup- tured/blocked blood vessels are repaired at the injury sites through surgery. During the procedure, some agents can be administered to initiate cell reprogramming and to rewire the neural circuitry. In some other diseases, cell reprogramming can be used for both requirements. For example, in type I diabetes, the immune system destroyed the patient’s own cells, through a process that is still not fully understood. In this case, T cells can be first repro- grammed to Treg cells to stop the self-destruction,
References 1 Gurdon, JB. Adult frogs derived from the nuclei of single somatic cells. Developmental Biology 4, 256- 273 (1962). 2Takahashi, K and Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663- 676 (2006). 3 Zhou, Q, Brown, J, Kanarek, A. Rajagopal, J and Melton, DA. In vivo reprogramming of adult pancreatic exocrine cells to - cells. Nature 455, 627-632 (2008). 4Vierbuchen, T, Ostermerier, A, Pang, ZP, Kokubu, Y, Südhof, T and Wernig M. Direct conversion of fibroblasts to functional neurons by defined factors.
Doi:10.1038/nature08797 (2010), 5 Ieda, M, Fu, JD, Delgado- Olguin, P, Vedantham, V, Hayashi, Y, Bruneau, BG and Srivastava, D. Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors. Cell 142, 375-386 (2010). 6Waddington, CH. The strategy of the genes. A discussion of some aspects of theoretical biology. Alen & Unwin, 1957. 7 Davidson, EH. The regulatory genome: gene regulatory networks in development and evolution. Academic Press, USA, 2006. 8Warren, L, Manos, PD, Ahfeldt, T, Loh, Y-H, Li, H, Lau, F, Ebina, W, Mandal, PK, Smith, ZD, Meissner, A, Daley, GQ, Brack, AS, Collins, JJ, Cowan, C, Schlaeger, TM and Rossi, DJ. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell 7, 618- 630 (2010). 9Wadia, JS and Dowdy, SF. Protein transduction technology. Current Opinion in Biotechnology 13, 52-56 (2002).
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