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Profiling expression heterogeneity

The use of cultured cell lines in cancer research is very common; however, it is unclear how much they recapitulate the cellular heterogeneity observed among malignant cells in tumors due to the absence of a native tumor microenvironment. Dr. Itay Tirosh and his research group in the Department of Molecular Cell Biology at the Weizmann Institute have developed a cost-effective method to profile expression heterogeneity by multiplexing single cell RNA-seq samples. The dataset revealed recurrent expression programs that are heterogeneous within many cancer cell lines and are primarily driven by epigenetic plasticity (and not genetics).

The Crown Institute for Genomics took part in the project by enabling solutions for both single cell RNA-seq (10x genomics) as well as gene expression measurements from both a large and a small amount of input material. Further work at the Maurice and Vivienne Wohl Institute for Drug Discovery has evaluated the sensitivity of some of the cell populations to drugs.

Reducing turnaround time

Reduction of turnaround time is on of our goals in the de Botton Protein Profiling unit.
Lately, we were able to reduce the average turnaround time is now 18 days, with small scale experiments being completed in less than 14 days.

This significant reduction in turnaround time is due to additional staff and two more LC-MSMS systems, for a total of five fully operational LC-MSMS systems.

Glycoproteomics workflow

A new instrument, Tribrid Orbitrap Fusion Lumos Mass Spectrometer, was introduced to the unit during this year. This new equipment enables faster analysis, sample multiplexing, which is optimal for the localization of posttranslational modifications, and enables new applications such as top-down proteomics.

One of the unique capabilities of the new instrument (pictured below with samples of data produced) is the analysis of proteins containing carbohydrates as a posttranslational modification. This modification is critical in various diseases, and it was important to set up a workflow in preparation of the collaboration with Dr. Michal Beeri from the Sheba Medical Center. This collaboration will involve the analysis of glycoproteins and glycopeptides in order to develop serum glyco-profiles of human subjects with type II diabetes and Alzheimer’s disease (AD).

 

Working on diabetes

Dr. David Morgenstern, a scientist at the de Botton Protein Profiling Unit, led a project that managed to identify 262 glycosylation sites, 259 glycoforms, and 51 completely novel glycans.

The next stage is to analyze 80 serum samples collected from type II diabetes patients, who have been monitored for several years. Some of these patients developed Alzheimer’s disease. The team will compare their serum glyco-profiles with diabetics who did not develop AD and healthy controls.