The Cellular Logic of Phenotype The goal of this application is to develop a strategy for predictably and reproducibly altering the phenotype of primary cells in culture. Differentiated cell types differ from each other in their RNA profiles (relative as well as absolute abundances of the RNAs they express). I hypothesize that, by the transferring entire RNA profiles from donor to recipient cells in a way that makes the recipient cells'survival dependent on donor RNA, the donor RNA will change the recipient into a destination phenotype that mimics the donor cell phenotype. This procedure is called Transcriptome Induced Phenotype Remodeling (TIPeR). Having the ability to transfer cell phenotypes between cells would provide important new insights into mechanisms controlling cell differentiation. The theory and technical strategies to accomplish this are being developed in my laboratory. Specifically, using laser light induced phototransfection (developed in my lab), we transiently produce pores in the host primary cell, through which RNA populations (in which RNA species and abundances are carefully controlled), can diffuse. Preliminary data shows that donor cell RNA populations carry """"""""memory functions"""""""" in that, donor RNA can induce long-term changes in genomic transcription of the host cells thereby changing the functional phenotype of the host cells to that of the destination phenotype. This is due in part to the activity and abundances of the specific proteins made from the host cell RNA mixture. Through developing various high- throughput quantitative """"""""Omics"""""""" level phenotyping technologies coupled with the TIPeR procedure it is anticipated that the """"""""genomics logic"""""""" of phenotype will be discerned. An understanding of this logic will permit the creation of specific cell types at will. The ability to selectively and rationally create cellular phenotypes promises to provide important insights into the fundamental mechanisms underlying cellular polarity, functioning and phenotype stability and may yield novel """"""""individualized medicinal therapeutics"""""""".

National Institute of Health (NIH)
National Institute of Mental Health (NIMH)
NIH Director’s Pioneer Award (NDPA) (DP1)
Project #
Application #
Study Section
Special Emphasis Panel (ZGM1-NDPA-B (P2))
Program Officer
Beckel-Mitchener, Andrea C
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Pennsylvania
Schools of Medicine
United States
Zip Code
Buckley, Peter T; Khaladkar, Mugdha; Kim, Junhyong et al. (2014) Cytoplasmic intron retention, function, splicing, and the sentinel RNA hypothesis. Wiley Interdiscip Rev RNA 5:223-30
Lovatt, Ditte; Ruble, Brittani K; Lee, Jaehee et al. (2014) Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue. Nat Methods 11:190-6
Kim, Tae Kyung; Sul, Jai-Yoon; Helmfors, Henrik et al. (2013) Dendritic glutamate receptor mRNAs show contingent local hotspot-dependent translational dynamics. Cell Rep 5:114-25
Morris, Jacqueline F; Sul, Jai-Yoon; Kim, Min-Sun et al. (2013) Elk-1 phosphorylated at threonine-417 is present in diverse cancers and correlates with differentiation grade of colonic adenocarcinoma. Hum Pathol 44:766-76