Cell Arrays for Measuring Cell Arrays for Measuring Gene Function on a Genomic Gene Function on a Genomic

ScaleScaleEdward Marcotte, Ph.D.Edward Marcotte, Ph.D.

Department of Chemistry and Department of Chemistry and BiochemistryBiochemistry

Cell-based assaysCell-based assays

Replacing traditional enzyme or Replacing traditional enzyme or antibody-based assaysantibody-based assays• The cell is the minimum physiological unit The cell is the minimum physiological unit

in the body.in the body.

• Greater accuracy is obtained when Greater accuracy is obtained when measuring drug action.measuring drug action.

• Activity is monitored in the context of a Activity is monitored in the context of a living, dynamic environment.living, dynamic environment.

Opportunities and challengesOpportunities and challenges

Cell-based assays are central to:Cell-based assays are central to:• Drug discovery programsDrug discovery programs

• Toxicology and initial ADME studiesToxicology and initial ADME studies

• Drug re-work effortsDrug re-work efforts

Cell-based assays have inherent Cell-based assays have inherent limitations. limitations. • Capacity of samplesCapacity of samples

• Adaptability to new assaysAdaptability to new assays

Need to meet expanding marketNeed to meet expanding market• Cell-based assay market is >$1 billion/year.Cell-based assay market is >$1 billion/year.Genetic Engineering News

A new approach to cell-based A new approach to cell-based assaysassays

Plates of cells for analysis

50-100 single-use

assayplates

One cell chip slide

(multi-assay)

OR

Our solutionOur solution

A cell-based chip:A cell-based chip:• Array up to 10,000 different cell variants on a Array up to 10,000 different cell variants on a

microslidemicroslide• Map coordinates of cell spotsMap coordinates of cell spots• Perform desired assayPerform desired assay

Applications:Applications:• Analyze multiple drugs on single cell typeAnalyze multiple drugs on single cell type• Analyze single drug on thousands of cell typesAnalyze single drug on thousands of cell types• Living or fixed cellsLiving or fixed cells• Simultaneous analysis of:Simultaneous analysis of:

Entire bacteria or yeast knockout librariesEntire bacteria or yeast knockout libraries Human RNAi knock-down librariesHuman RNAi knock-down libraries Human/yeast GFP-tagged protein librariesHuman/yeast GFP-tagged protein libraries

Cell chip fabricationCell chip fabrication

Plates of cells for analysis

Cell chip

Close-up view

Robotic spotting of cells on microscope slide

~4,800 cells / slide~20-40 cells / spot~100 slides / batch

Example: Protein subcellular Example: Protein subcellular localization localization

GFP-taggedcell library

Printcell chips

Identify subcellularlocalization of eachGFP-tagged protein

>500,000 assays performed to date

White lightNucleus

stainCell surface

stainVisualized

proteinProtein namelocalization

BenefitsBenefits

Applicable with bacterial, yeast, and mammalian cellsApplicable with bacterial, yeast, and mammalian cells Small amounts of reagents expendedSmall amounts of reagents expended

• Enabling rare cell and limited compound analysisEnabling rare cell and limited compound analysis

Amenable to many assays:Amenable to many assays:• Protein localization and dynamic transportProtein localization and dynamic transport

• High-content, fluorescence assays High-content, fluorescence assays

• Drug effect assays, cyto-toxicity Drug effect assays, cyto-toxicity

• Apoptosis Apoptosis

• Cell proliferation Cell proliferation

Flexible format, easy storageFlexible format, easy storage Applications in drug discovery and genetic network Applications in drug discovery and genetic network

researchresearch U.S. and PCT patents filed covering technologyU.S. and PCT patents filed covering technology