1 Biomaterials Evolution This platform will create massively-parallel capabilities for directed evolution of biomolecules, such as DNA, for regenerative medicine and bioenergy Wyss Faculty Lead: George Church Other Wyss Faculty: Pam Silver William Shih Jim Collins Don Ingber Overall Goals: Directed Evolution of Human Antibodies Multi-Gene Switches for Cell Reprogramming DNA as a Cost Effective Biomaterial

2 Biomaterials Evolution Platform DNA Synthesis, assembly & analysis on chips -DNA as a Cost Effective Biomaterial (Shih) -Human Antibody & Antigen Libraries (Ingber) Directed Evolution of Microbial Communities -Metabolic engineering fuels, chemicals (Silver, Collins) Gene Switches for Human Cell Reprogramming -Combinatorial Control of Stem Cell & Cancer Cell Differentiation (Ingber & Collins)

3 Sequencing tracked Moore’s law 2X/2 yr until ,000x/4yr 2009 goal of 2% for $200 (coding + regulatory) $/bp 2005 $50M 2009 $5K

4 Open-architecture hardware, software, wetware Polonator $150K - 2 billion beads/run e.g IBM PC Rich Terry Senior Engineer

5 DNA Synthesis, assembly & analysis on chips Nitrobenzyl linkers for selective release of beads or cells Digital micromirror & inkjet

6 Biomaterials Evolution Platform DNA Synthesis, assembly & analysis on chips -DNA as a Cost Effective Biomaterial (Shih) -Human Antibody & Antigen Libraries (Ingber) Directed Evolution of Microbial Communities -Metabolic engineering fuels, chemicals (Silver, Collins) Gene Switches for Human Cell Reprogramming -Combinatorial Control of Stem Cell & Cancer Cell Differentiation (Ingber & Collins)

7 Antibody ( & TCR) VDJ regions N H J H J  V H *D H *N H *J H *V  *J  N *23*N * 6 * 67* 5 = > 2M combinations, 750 bp, >1E10 cells

Antibody- antigen pair selection Ribosome-display for biomimetic-microsystems antigens Antigen mRNA VDJ mRNA

9 Biomaterials Evolution Platform DNA Synthesis, assembly & analysis on chips -DNA as a Cost Effective Biomaterial (Shih) -Human Antibody & Antigen Libraries (Ingber) Directed Evolution of Microbial Communities -Metabolic engineering fuels, chemicals (Silver, Collins) Gene Switches for Human Cell Reprogramming -Combinatorial Control of Stem Cell & Cancer Cell Differentiation (Ingber & Collins)

10 Re-programming adult human cells to multiple tissues with combinations of DNAs Hair or skin sample

11 Viral delivery: β-catenin, Dnmt3l, Dppa2,3,4,5, Ecat1, Eras, Fthl17, Grb21, Ecat8, Fbx15, Gdf3, hTERT, Klf4, Myc, Nanog, Oct4, Rex1, Sall4, Sox2, Sox15, Stat3, Tcl1, Utf1 Signals: Activin, BMP4, Estrogen, FGF, HGF, PDGF, Retinoate, Shh, TGF, VEGF. Combinations of regulatory genes Cartilage & bone Respiratory epithelium Immature Brain Skin-derived stem cells

12 Biomaterials Evolution Platform DNA Synthesis, assembly & analysis on chips -DNA as a Cost Effective Biomaterial (Shih) -Human Antibody & Antigen Libraries (Ingber) Directed Evolution of Microbial Communities -Metabolic engineering fuels, chemicals (Silver, Collins) Gene Switches for Human Cell Reprogramming -Combinatorial Control of Stem Cell & Cancer Cell Differentiation (Ingber & Collins)

Genome Engineering Multiplex Automation (GEMA) instrument For metabolic optimization of fuels, biochemicals, pharmaceuticals

14 Accelerated evolution for valuable metabolites & biofuels

WIBIE Silver Lab Efforts Silver Lab DNA as a Cost- Effective Biomaterial Directed Evolution of Human Antibodies Multi-Gene Switches for Cell Reprogramming Designer proteins for assembly into nanostructures (with Ingber) In silico design of “DeImmunized” antibody libraries (with Church) Engineered cellular memory and logic (with Collins/Ingber) Quantitatively designed protein therapeutics Engineered electron transfer for bio-energy Adaptive architecture/ nanomaterials

16 9:05-9:35 4-Feb-2009 Wyss Institute for Biologically Inspired Engineering Thanks to: Poised for Industrial Collaborations