Jim Eberwine and I am involved in various aspects of single cell biology.

Cell differentiation

We have been using the idea that RNA of a cell is a key tunable part of the molecular state space and whole transcriptomes can be used to trans-differentiate one cell type to another (Kim and Eberwine, 2010, Trends in Cell Biol. DOI: 10.1016/j.tcb.2010.03.003). Using laser-mediated phototransfection, we showed that differentiated neurons in rats can be made to acquire the stable phenotype of differentiated astrocytes (Sul et al. 2009 PNAS doi: 10.1073/pnas.0902161106). We are now working to generalize this process to other cell types and to develop new combinatorial process to systematically explore the idea of cell type tuning.

Genomic factors for subcellular localization

Many molecules in a cell act in a spatially localized manner. In particular, specific RNA in neurons translocate to dendrites and axons and serve as templates for local translation in response to external signals. We are studying the sequence/structure factors that mediate this localization at the whole genome scale. We have found that many mRNA contain subsequences of introns that are retained when exported to the cytoplasm (CIRTs; Cytoplasmic Intron-sequence Retained Transcripts). Some of these CIRTs seem to contain signaling factors including localization signals. Our hypothesis is that the CIRTs mediate subcellular processes and are cytoplasmically spliced out before translation.

Single cell RNA variability in human brain cells

Fully differentiated cells display heterogeneity in function, responses, and dysfunction. For example, both normal and disease-related cognitive decline involve select brain subsystems and differential dysfunction at the cellular level. The adult heart shows differential cellular responses to cardiac infarction and has distinct subpopulations of cells including those that support regeneration. Increasing ability to discriminate molecular states, especially levels of gene expression, has revealed molecular heterogeneity underlying seemingly homogeneous phenotypes at all levels down to the level of single cells. Many models and hypotheses have been generated to explain cellular heterogeneity. We are one of the three NIMH funded Single Cell Analysis Project-Transcriptomics U01 centers (see We are working with Penn Neurosurgery Group to isolate live brain cells from patients undergoing neurosurgery and profile single cell transcriptomes.