CBEE Seminar with Dr. Siddharth Dey, Hubrecht Institute

Chemical Biochemical Environmental Engineering Department Presents: 

Dr. Siddharth Dey 

Hubrecht Institute, The Netherlands 

Friday, February 26

10:00AM

UC 310, UMBC

Biography

Siddharth Dey graduated from the Institute of Chemical Technology (Formerly: UDCT), Mumbai in 2006 with a B.S. in Chemical Engineering. Next, he worked with Professor David Schaffer and Professor Adam Arkin and received his Ph.D. in Chemical and Biomolecular Engineering in 2012 from the University of California, Berkeley. During his graduate studies, he used quantitative single-cell techniques to investigate how the decision between a latent and lytic state in Human Immunodeficiency Virus-1 (HIV-1) is regulated by gene expression variability. In 2012, he moved to Professor Alexander van Oudenaarden's group as a post-doctoral researcher at the Hubrecht Institute, The Netherlands. Expanding upon this graduate work to study cellular heterogeneity on a genome-wide scale, he developed the first integrated single-cell genomics method that enabled sequencing both genomic DNA and mRNA from the same cell.

Abstract 

"Developing Novel Single-Cell Sequencing Technologies to Study Cellular Heterogeneity"

A central question in biology is to understand how variability in the genome or epigenome regulates gene expression heterogeneity, thereby influencing cellular functions. While heterogeneity in gene expression between individual cells has been studied extensively, with important biological consequences ranging from drug resistance in bacteria and tumors to biasing lineage choices in differentiating mammalian progenitor cells, the upstream mechanisms regulating cell-to-cell heterogeneity have been difficult to study and are poorly understood. 

To elucidate this relationship, I will be describing three studies where we developed novel single-cell technologies to understand how the genome and epigenome regulates the dynamics of gene expression. To understand how the local chromatin environment regulates gene expression variability, we combined stochastic modeling and DNA accessibility measurements with single-molecule mRNA FISH to show that more repressed chromatin is associated with increased heterogeneity in gene expression. These results have important implications for understanding viral latency. 

Next, we developed the first genome-wide technology that enabled sequencing both genomic DNA and mRNA from the same cell. We used this technology to show that low genomic copy number regions are associated with increased gene expression variability between individual tumor cells, suggesting that copy number variations may be a mechanism to tune cell-to-cell heterogeneity in gene expression.

 Finally, I will describe a new genome-wide single-cell method for quantifying the DNA modification 5-hydroxymethylcytosine (5hmC), which has recently been shown to have critical roles in development and gene regulation. Using this method, we discovered pronounced cell-to-cell variability in the relative amounts of 5hmC on the two DNA strands of a chromosome in mouse embryonic stem cells and 2-cell mouse embryos. By combining these results with a stochastic model, we demonstrated that even isogenic cell populations exposed to identical environments can display pronounced chromosome-wide epigenetic heterogeneity due to the slow kinetics of 5hmC turnover. Thus, these studies are beginning to reveal fundamental new insights into how variability in the genome or epigenome influences cellular heterogeneity and ultimately, cellular phenotypes.

 Finally, I will briefly discuss future research plans where I propose to develop novel integrated single-cell sequencing technologies that enable simultaneous genome-wide measurements of the epigenome and transcriptome from the same cell to gain insights into tumor evolution and progression, early mammalian development, and mechanisms regulating the maintenance and regeneration of adult tissues, knowledge that will be critical to more efficiently direct differentiation for regenerative medicine applications.