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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

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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)

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Sequencing tracked Moore’s law 2X/2 yr until 2005-9 10,000x/4yr

2009 goal of 2% for $200 (coding + regulatory)

0.0000001

0.000001

0.00001

0.0001

0.001

0.01

0.1

1

10

1990 1995 2000 2005 2010

$/bp 2005 $50M

2009 $5K

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Open-architecture hardware, software, wetware

Polonator

$150K - 2 billion beads/run

e.g.1981IBM PC

Rich TerrySenior Engineer

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DNA Synthesis, assembly & analysis on chips

Nitrobenzyl linkers for selective release of beads or cells

Digital micromirror & inkjet

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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)

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Antibody (& TCR) VDJ regions

VH*DH*NNHH*JJHH*V*JJ

46*23*N N * 6 6 * 67* 55 = > 2M combinations , 750 bp, >1E10 cells

Antibody- antigen pair selectionRibosome-display for

biomimetic-microsystems antigens

Antigen mRNA

VDJ mRNA

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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)

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Re-programming adult human cells to multiple tissues with combinations of DNAs

Hair or skin sample

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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, Utf1Signals: Activin, BMP4, Estrogen, FGF, HGF, PDGF, Retinoate, Shh, TGF, VEGF.

Combinations of regulatory genes

Cartilage & bone

Respiratory epithelium

Immature Brain

Skin-derived stem cells

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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

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Accelerated evolution for valuable metabolites & biofuels

WIBIE Silver Lab Efforts

Silver LabDNA 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

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9:05-9:35 4-Feb-2009 Wyss Institute for Biologically Inspired Engineering

Thanks to:

Poised for Industrial Collaborations