Shalin Naik-Projects

Shalin Naik-Projects

Researcher: 

Projects

Using cellular barcoding to track individual stem and progenitor cells in vivo

Cellular barcoding is a technology that allows the tracking of fate for hundreds of single stem cells simultaneously. Each progenitor is tagged with a unique DNA ‘stamp’ such that it is inherited by daughter cells and detected in progeny using DNA sequencing and computational analysis. In this way, we can compare barcode inheritance between cell types to infer their derivation from common vs. separate ancestors. We have used the technique to decipher the complexity of their individual fate and to reconstruct single cell lineage decisions in haematopoiesis (Naik, Nature, 2013). We are now covering other aspects of haematopoiesis, including how these patterns change upon duress such as infection, and how modification of genetic regulators affects the output of single cells.

Team members: Dawn Lin, Jaring Schreuder, Gabrielle Mitchell, Sangeetha Ramdave

Constructing pedigrees from single stem cells using long-term imaging

While cellular barcoding can determine the fate of many single cells in vivo, it cannot provide information on the shape of the ‘family tree’ where a single stem cell generates multiple cell types. In order to decipher this tree, one must track the entire process, including division and differentiation, and without loss of identity of individual cells. To achieve this, we image microwells containing hematopoietic progenitors every 1-2 minutes for five days. In this system we can identify the acquisition of particular fates by cells by including fluorescently-labeled antibodies in the culture medium. 

Team member: Dawn Lin

Using single cell RNA-sequencing to identify lineage programs

We have previously established that haematopoietic progenitors with very similar phenotypes often exhibit highly heterogeneous fates. Through clone-splitting experiments, where the fates of siblings from a single cell are assessed independently (for example, in two separate wells in vitro or transferred to two recipients in vivo), we have determined that this heterogeneous fate is often ‘imprinted’ (Naik et al. Nature. 2013). We are tackling the nature of these molecular programs by performing high throughput single cell RNA sequencing – a relatively new but powerful technique – that can reveal single cell resolution differences that may account for differences in fate.

Team members: Jessica Tran, Daniela Zalcenstein, Sangeetha Ramdave