Ido Amit, AmitLab @Department of Immunology at the Weizmann Institute of Science, Rehovot, Israel

The Amit lab studies the genomic code enabling immune cells to differentiate to specific subtypes and devise a specific response to invading pathogens. Our main focus is to understand how gene regulatory networks activate this code. We develop and apply state of the art high throughputgenomic tools and interdisciplinary approaches to address these critical biological and therapeutic questions. We believe that elucidating the underlying principles of the regulatory code will allow us to impact the future of personalized medicine. We are currently seeking highly motivated individuals who want to join us on this quest.

SOURCE

https://www.weizmann.ac.il/immunology/AmitLab/front

Immunology, one cell at a time

03 July 2017

• Amir Giladi
• & Ido Amit

Basic lessons – “Single-cell genomics will soon be commonplace in basic and applied immunology research.”

It is early days for single-cell genomics. But already, a number of important lessons can be learnt from the experiences of our lab and those of others.

First, it is clear that many of the current categories of immune cells, such as T cells or monocytes, encompass heterogeneous populations. To probe cellular complexity, researchers must therefore cast their nets wide, and try to collect all immune cells within a tissue or region of interest. This is a very different approach from that used with methods based on cell-surface markers, which aim to obtain as pure a sample as possible.

Second, success will depend, in part, on the extent to which researchers preserve the states of cells and the original composition of a tissue. Cell stress or death should be minimized to ensure that tissue preparation does not favour specific cell types. (Some are more sensitive to heat stress, for example, than others.)

Third, bioinformaticians will need to develop scalable and robust algorithms to cope with greater numbers of cells, conflicting or overlapping programs of gene expression and fleeting developmental stages.

Fourth, after researchers have characterized all of the immune cells in a sample, they will need to find molecular markers that can be used to either enrich or deplete certain cell types in further samples. Tissues comprise trillions of cells with myriad molecular characteristics and functions, and the types or states of these cells may vary in abundance by many orders of magnitude. For instance, in the brains of healthy mice, our newly identified population of DAM makes up less than 0.01% of cells¹⁵. Thus, repeated unbiased sampling to characterize rare populations will keep on accumulating cells that are not those of interest.

Nature 547, 27–29 (06 July 2017) doi:10.1038/547027a

http://www.nature.com/news/immunology-one-cell-at-a-time-1.22232?WT.ec_id=NEWSDAILY-20170703

 Ido Amit – Selected References