Lecture 2: Nuclear Reprogramming

1. Lecture 2: Nuclear Reprogramming

2. Nuclear Reprogramming Switch of gene expression from one cell typeto another Switch from a differentiated, specialized cell type to a developmental more primitive and pluripotent state • No modification of the genome • Alteration of the epigenome (DNA methylation, histone modification)

3. How to reprogram towards pluripotency Somatic cell nuclear transfer Somatic cell fusion with pluripotent cells Transduction of pluripotent genes into somatic cells a.k.a. Direct reprogramming Yamanaka and Blau, Nature, 465(7299):704{12, Jun 2010.

4. History of nuclear reprogramming nuclear transfer (blue), cell fusion (pink) and transcription-factor transduction (green) Yamanaka and Blau, Nature, 465(7299):704{12, Jun 2010.

5. How to reprogram towards pluripotency(reminder) Somatic cell nuclear transfer Somatic cell fusion with pluripotent cells Transduction of pluripotent genes into somatic cells Yamanaka and Blau, Nature, 465(7299):704{12, Jun 2010.

6. Somatic-derived stem cells via nuclear transfer Nucleus directed differentiation • Create ES cells that match the donor’s genetic makeup for therapeutic purposes. • Currently, no human ES stem cell lines have been derived from this method (only 3N so far). • ES cells derived from patients can be directed to differentiate into specific lineages (e.g. dopaminergic neurons) to study a particular disease (e.g. Parkinson’s disease). • This method may be used for cell-based therapies that would circumvent immune rejection. • Not extensively used at present, because: 1) iPS strategies are more feasible, 2) stress to the egg causes a reduced efficiency for ES cell generation, 3)ethics. Fibroblasts from patients Enucleated oocyte ES cell Progenitor Neuron

7. How to reprogram towards pluripotency (reminder) Somatic cell nuclear transfer Somatic cell fusion with pluripotent cells Transduction of pluripotent genes into somatic cells Yamanaka and Blau, Nature, 465(7299):704{12, Jun 2010.

8. Cell Fusion-Mediated Nuclear Reprogramming • Several nuclei are forced to share one common cytoplasm (viral, chemical or electric cell fusion technologies) • If fused cells proliferate they will become hybrids and on division the nuclei fuse to become 4n or greater • Ratio of different nuclei and culture medium conditions favors towards the desired cell type. • Direct and fast method (1-2 days)

9. How to reprogram towards pluripotency Somatic cell nuclear transfer Somatic cell fusion with pluripotent cells Transduction of pluripotent genes into somatic cells Yamanaka and Blau, Nature, 465(7299):704{12, Jun 2010.

10. Induced pluripotent stem cells (iPS cells) 10

11. Induced pluripotent stem cells (iPS cells) Skin cell iPSC With few reprogramming factors OCT3/4, SOX2, KLF4, cMYC OCT3/4, SOX2, LIN28, NANOG Yamanaka factors Thomson factors Reprogramming Strategy • A type of pluripotent stem cell artificially derived from an adult somatic cell by "forcing" expression of specific genes. • Forced expression in somatic cells is realized by: • Viral transduction • Proteins • Plasmids • mRNA 11

12. iPS cells – using retrovirus/lentivirus Advantages: - easy to use - reproducible - good efficiency - controlled expression (inducible) Disadvantages: - increased risk of insertional mutagenesis - possibility of transgene reactivation - incomplete silencing - clone to clone variation 12

13. iPS cells – using Proteins Advantages: - no genomic modification - non-DNA approach Disadvantages: - very slow process - very inefficient process (0.006%, Zhou et al. 2009) - requires the addition of other molecules (VPA) • Reprogramming factors are fused to cell-penetrating peptide (CCP) • Proteins can be recombinant (produced in bacteria) or in mammalian cells (HEK293) • Proteins need to be active and functional in order to work 13

14. iPS cells – using Plasmids Advantages: - no genomic modification Disadvantages: - very inefficient process (0.006%, Zhou et al. 2009) - repeated transfection 14

15. iPS cells – mRNA Advantages: - no genomic modification - highly efficient approach - faster kinetics - factors titratable - transient nature of mRNA - Biosafety Disadvantages: - repeated transfection 15

16. Nuclear reprogramming with mRNA Day 1 Day 3 Day 5 Day 7 Day 9 Day 10

17. iPS cells - a recent advance • it allows researchers to obtain pluripotent stem cells, which are important in research and potentially have therapeutic uses, without the controversial use of embryos. • Reprogramming adult cells to obtain iPS cells may pose significant risks that could limit their use in humans. If viruses are used to alter the cells’ genome, the expression of cancer-causing genes or oncogenes may potentially be triggered after these cells are introduced into animals. 17

18. iPS cells versus ES cells RNA iPSC • iPS cells are believed to be similar to ES cells with respect to: • A) stem cell gene and protein expression • B) ability to differentiate into all lineages in vitro • C) forming viable chimeras after injection into blastocysts or tumors when transplanted into adult tissues • D) potential to form an entire organism, such as a mouse Embryonic stem cell

19. iPSCreprogramming factors • Retroviruses (viruses that contain RNA, and convert RNA into DNA) that infect fibroblast cells are commonly used. • Virus encodes four transcription factors: Oct4, Sox2, Klf-4 and c-Myc. C-Myc is a tumor-inducing gene (oncogene). • Oct4 and Sox2 are necessary to induce pluripotency of fibroblasts. • Transcription factors increase the efficiency of iPS production. • Currently, reprogramming is inefficient and slow. • Transcription factors modify gene expression in infected cells. • Factors turn OFF genes that are part of the differentiated phenotype. • Factors turn ON genes that both maintain pluripotency and the ability to self-renew. 19

20. iPSCreprogramming factors – OCT3/4 • transcription factor (one slide of what a transcription factor is!!!) • key reprogramming factor for derivation of iPS cells • master regulator of pluripotency • specifically expressed in ES cells and the early embryo • knock-down of OCT3/4 in ES cells leads to differentiation • to date specific function of OCT3/4 during reprogramming is not known 20

21. iPS reprogramming factors – SOX2 • another key factor for nuclear reprogramming • expressed in ES cells, early embryos, germ cells and neural stem cells • May act as an OCT3/4 cofactor and even regulate expression of OCT3/4 itself • SOX2 forms heterodimers with OCT3/4 to synergistically control ES cell-specific gene expression 21

22. Reprogramming different cell types 22 Sun et al., 2010

23. Epigenetic modifications during reprogramming 23

24. What exactly happens during reprogramming? Suggested model #1 Suggested model #3 Suggested model #2 24

25. Transcriptional Regulatory Circuitry Suggested model #1 Suggested model #2 25

26. Nuclear ReprogrammingConcept Mapping Terms Add the key terms/concepts from today’s lecture to your previous concept map. You should include (but are not limited to) the following terms/concepts: Induced pluripotent stem cell Nuclear transfer Transcription factor Direct reprogramming Reprogramming factor Epigenome Transgene Transcriptional Regulatory Circuitry Yamanaka factors Due by xxx 26