transcription factor profiling in individual hematopoietic progenitors by digital rt-pcr luigi...
TRANSCRIPT
Transcription factor profiling in individual hematopoietic
progenitors by digital RT-PCR
Luigi Warren, David Bryder, Irving L. Weissman, and Stephen R. Quake
Background
• Stem cell differentiation– Chemical state machine• Sequencing logic implemented by cross-regulating
transcription factors• State of the network realized in the abundance profile
of these regulatory molecules
– Transitions between states• Instability, stochastic fluctuation, external signals
– Transcription factor PU.1• Cytokine receptor flk2• Housekeeping transcript GAPDH
Early Progenitors in the Hematopoietic Lineage Tree
Goals
• Understand the behavior of transcriptional regulatory network for stem cell differentiation– Leads to understanding of development– Requires the ability to characterize network states
quantitatively
Problems
• Network states cannot be characterized quantitatively– Current gene profiling methods not sensitive enough
• Conventional gene expression assays– Stem cells not easily isolated in such quantities– Require thousands of cells’ worth of RNA as analyte– Population-average expression data provide an
incomplete picture• Variations in network state determined by just a few
phenotypic differences between cell types
Conventional PCR
• Quantitation based on number of cycles required for dye fluorescence to reach given threshold
• Exponential nature magnifies slight variations in amplification efficiency
• Interassay comparisons only valid if gene-of-interest measurements are normalized to measurements on endogenous controls or synthetic standards
Solution• Digital RT-PCR– Partition individual cDNA molecules
into discrete reaction chambers before PCR amplification
– Quantitation uses binary, positive/negative calls for each subreaction within partitioned analyte
• Flow Cytometry– Reveals diversity in patterns of surface
protein expression within populations of superficially similar cells
Expression Profiling for CMP
FACS
• Fractionation of CMP cells into flk2+ and flk2- subsets
Digital Array Chip
• cDNA from individual HSCs
• Green: GAPDH
• Red: PU.1• Each well
captures ~0 or 1 template molecules
Results
• Number of individual cells expressing PU.1• PU.1 expression up-regulated in CMP/flk2+
• Down-regulated in CMP/flk2- cells and MEPs• Higher GAPDH expression in CMPflk2+cells.
Further Optimizations
• Threshold values• Reference endogenous controls– Weighted normalization of data
• mRNA vs protein turnover rate• Measurement noise
Future Application
• Gene expression measurements can be made on an absolute, copy-number-per-cell basis
• Sophisticated regulatory network analysis• Spread of public databases cataloguing cell-
type-specific expression data• Refinement of taxonomies through single-cell
survey approach
Thank you
• Questions?