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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.

Splice isoform switching

The team at the Crown Institute for Genomics has collaborated with the Bar-Ilan University lab of Dr. Tomer Kalisky in order to study gene expression during kidney development. Stem cells in the kidney undergo mesenchymal to epithelial transition (MET), followed by a series of differentiation events that eventually create the various cell types that constitute the developed kidney. Using the Smart-seq2 method adopted by the G-INCPM genomics team, the scientists performed single-cell RNA sequencing on hundreds of individual cells. They were able to detect splice isoform switching events that occur during development, shedding more light both on kidney differentiation, and on the “reverse” process of renal tumorigenesis.


Embryo development

In a project conducted with Dr. Jacob Hanna of the Weizmann Institute’s Department of Molecular Genetics, scientists at the Crown Institute for Genomics team examined molecular factors that affect embryo development in early stages. Applying the Smart-seq2 protocol to embryonic cells at the 2-cell stage, the scientists obtained high-resolution gene expression profiles of these cells. Such data can provide a deeper understanding of embryonic development.

Our new NanoString nCounter

The Crown Institute for Genomics has acquired a new instrument, the NanoString nCounter® FLEX. This instrument provides a simple and cost-effective solution of direct digital quantification for multiplex analysis of up to 800 known RNA, DNA, or protein targets in one tube. The quantification is done directly on the molecular target and avoids biases introduced by enzymatic reactions (e.g. reverse transcription, amplification or ligation). It is ideal for a range of applications requiring efficient, high-precision quantitation of hundreds of target molecules across a sample set.

Biomarkers in myelodysplastic syndromes patients

Using the Smart-seq2—a technology available at the Crown Institute for Genomics which sequences sigle cell full transcripts and allows detection of more genomic changes than other single cell methodologies—we worked with Dr. Roi Gazit from the National Institute for Biotechnology in Ben-Gurion University of the Negev. We sequenced the mRNA of MDS patients.

Smart-Seq2 protocol, developed by Dr. Simone Picelli at Prof. Rickard Sandberg's lab, allows detailed analysis of splicing, something known to play a major role in the initiation and progression of MDS. The team indeed observed differences in splicing, as well as variations in nucleotide sequences (SNP) in single hematopoietic (blood forming) stem cells of MDS patients. By correlating this molecular data with disease progression of MDS patients treated at the Soroka Medical Center, the observed variations could be used as biomarkers for evaluating leukaemia risk.

Cardiac remodeling

The Crown Institute for Genomics team has collaborated with Dr. Izhak Kehat, a cardiologist and a researcher at the Faculty of Medicine at the Technion, to understand gene expression in the heart at the single cell level. Heart cells (cardiomyocytes) present a major challenge for single cell sequencing techniques, due to their large dimensions and their dense and rigid cytoskeleton. The genomics team at the Crown Institute worked closely with Dr. Kehat in order to address the limitations of the heart tissue, using the Smart-seq2 protocol. As a result, they were able to produce the first high quality single cell RNA sequencing of cardiomyocytes.

A new way to analyze paraffin embedded samples

The Crown Institute for Genomics team has collaborated with Dr. Maya Dadiani and Bella Kaufman from the Institute of Oncology in Sheba Medical Center and with Dr. Noa Bossel from the lab of Prof. Eytan Domany of the Weitzmann Institute. We analyzed gene expression from tumor tissues preserved in Formalin-Fixed Paraffin-Embedded (FFPE) blocks. The FFPE preservation method is routinely used in the world of oncology, and the ability to sequence mRNA from these samples opens a treasure trove of historic data for retrospective clinical studies. Nonetheless, mRNA sequencing from such samples is technically challenging and expensive, due to RNA degradation, and results from FFPE are typically of poor quality. The genomics team has established a reliable and cost-effective procedure sequencing RNA from FFPE samples, that can open the door for large-scale retrospective clinical studies.

The publication

MinION sequencer

In May 2017, Shlomit Gilad from the Crown Institute and Barak Markus from the Mantoux Institute for Bioinformatics) attended a users’ conference organized by UK-based Oxford Nanopore in London, where they learned about a scientific and technological breakthrough, the palm-sized gene sequencer that can read out relatively long stretches of genetic sequence. The MinION is portable, relatively inexpensive, and it plugs into the USB port of a laptop, displaying data on the screen as they are generated, rather than at the end of a run, which can take multiple days.  While the goal of sequencing a human genome in 15 days is yet to materialize, the new technology is highly suitable for de novo sequencing on bacteria, for example.

The genomics and bioinformatics team purchased the instrument and have been working together to validate the methodology.  In terms of error rate, this technology is still in its early stages in comparison to the already established sequencer from Pacific Biosciences. However, if ultimately successful, this technology does not rely on expensive infrastructure and costly equipment, and represents the wave of the future, where physicians and laboratory workers may perform sequencing in order to identify a bacterial strain in a human sample within minutes.

Image: Oxford Nanopore Technologies

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