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Rosenbluh Lab research

CollaborationsStudent research projects | Publications

About Associate Professor Joseph (Sefi) Rosenbluh

Associate Professor Joseph (Sefi) Rosenbluh is the head of the Cancer Functional Genomics Lab at the Department of Biochemistry and Molecular Biology at Monash University, and the scientific director of the MHTP Functional Genomics platform. After completing his PhD at the Hebrew University of Jerusalem, A/Prof Rosenbluh moved to the Broad Institute of Harvard and MIT as a postdoctoral fellow and later as an instructor of medicine. He joined the faculty of Monash University in November 2016. His recent focus has been on developing CRISPR technologies for high throughput genetic screens and applying these approached for understanding and treating cancer.


Our research

Research overview

Recent technological advances include CRISPR based technologies as well as advances in screening technologies are revolutionising our ability to use functional genomics. Research in the Rosenbluh lab uses state of the art functional genomic tools including pooled CRISPR loss/gain of function screens and apply these technologies towards identifying genes that are associated with cancer phenotypes as well as genes that could be used for development of new cancer treatments.

This figure shows the principle of pooled gain/loss of function screens. Advances in oligo synthesis technologies make it possible to synthesis up to 100,000 different sequences in just a few days. This enables very rapid generation of pooled sgRNA libraries that target every known human or mouse coding gene. Pooled libraries are then used to generate a pooled lentiviral library that is used to infect cells at low MOI (this insures that every infected cell receives only one virus). Following propagation genomic DNA is extracted and next generation sequencing is used to quantify sgRNA abundance.

Current projects

1. Systematic identification and validation of breast cancer risk genes through follow up of genome-wide association studies.
Using genome wide association studies (GWAS) our collaborator Prof. Georgia Chenevix-Trench (QIMR, Brisbane) and her team have identified 179 breast cancer (BC) risk loci (Michailidou et al. Nature, 2017). The functional mechanism behind the associations usually involves perturbed regulation of target gene transcription by risk single nucleotide polymorphisms (SNPs) lying in regulatory elements positioned some distance from the target. The nearest gene to the GWAS ‘hit’ is not necessarily the target of the association, and for some loci there are multiple gene targets. This project uses large scale pooled clustered regularly interspaced short palindromic repeats (CRISPR) knockout and activation screens of all the predicted target coding and non-coding genes at these loci. We will evaluate the effect of over-expressing or suppressing the expression of all candidate BC risk genes on the ability of cells to proliferate in vitro, and in immune-deficient mice, as well as their ability to promote bypass of cellular senescence, in order to identify determinants of BC risk. In addition to enhancing our understanding of the genetic variants associated with BC risk, these experiments will enable new strategies for risk reduction therapies.

This figure shows the overall strategy we are using to identify breast cancer risk genes that could be used for development of anti-cancer therapies and as biomarkers to identity women with high risk of developing breast cancer.

2. Identification of alternative transcripts that drive gastric cancer.
Gastric cancer is a leading cause of mortality. Currently only a limited number gastric cancer treatments are available and new treatment options are necessary. Our collaborator Prof. Patrick Tan (NUS-Duke, Singapore) used ChIP-Seq from normal and gastric cancers and has identified a class of genes that in gastric cancers are expressed from an alternative promoter (Qamra et al Cancer Discovery, 2017). Using a verity of CRISPR based approaches we are identifying alternative transcripts that are essential for proliferation of gastric cancer and could be used as targets for development of gastric cancer specific therapies.

This figure shows our strategy to identify new drug targets for gastric cancer therapy. (A and B) By comparing the abundance of H3K4me3 (a cellular mark of active transcription) in normal and gastric cancer our collaborator Prof. Patrick Tan and his team have identified thousands of gastric cancer specific transcripts. (C) Our strategy uses CRISPRi to supress the expression of canonical or alternative transcripts and identify new targets for gastric cancer therapy.

3. SRP19 as a target in APC deleted colon cancers.
Colon cancer remains a leading cause of mortality with only a limited number of treatment options. Although worldwide sequencing efforts revealed the landscape of genomic alterations that drive colon cancer we still lack approaches for direct targeting of most mutated oncogenes in colon cancer. Most notably, genomic alterations leading to inactivation of the tumour suppressor APC are found in ~80% of colon cancers. Furthermore, studies in cultured cancer cell lines and animal models demonstrate that contentious suppression of APC is required for tumour growth even in advanced metastatic colon cancer. However, despite the clear evidence demonstrating the importance of APC in colon cancer pathogenesis we currently lack approaches for direct targeting of tumour suppressors. An alternative approach is to identify genes that are required for proliferation only in the context of APC loss of function mutation. As a proof of principle for this strategy, previous work used genome scale shRNA loss of function proliferation screens and identified genes that are essential in cancers that harbour loss of a tumour suppressor gene. These experiment, identified a class of genetic vulnerabilities that are associated with DNA loss of a tumour suppressor we termed, CYCLOPS (Copy-number alterations  Yielding Cancer Liabilities Owing to Partial losS). Specifically, heterozygous loss of a tumour suppressor is accompanied by heterozygous deletion of neighbouring cell essential genes and as a consequence, the mRNA and protein levels of these neighbouring cell essential genes is reduced. Suppressing the residual expression of the cell essential genes inhibits proliferation only in cells that harbour loss of the tumour suppressor gene (See figure). Using this strategy, we identified SRP19, a component of the signal recognition complex, as a CYCLOPS in cancers that harbour APC loss. Mechanistically, SRP19 is located in close physical proximity (15kb) to APC and is lost in cancers that harbour APC loss. Our preliminary data show that cell lines and tumours that harbour APC loss have lower levels of SRP19 mRNA and protein and are highly sensitive to additional suppression of SRP19 expression. These observations suggest inhibitors of SRP19 as a strategy against cancers with APC loss. The overall aimof this project is to evaluate SRP19 as a therapeutic target in a specific population of colon cancers that harbour APC loss (~20% of colon cancers) and to develop strategies to inhibit SRP19 as an approach to treat these cancers. More generally, although this project is focused on targeting of colon cancers with APC loss the same approach could in principle be applied for targeting any tumour suppressor that is lost in cancer.

This figure shows the rational of targeting SRP19 in colon cancers that harbour heterozygous APC loss. Due to their close physical proximity loss of the tumour suppressor APC is accompanied by heterozygous loss of neighbouring SRP19, a cell essential gene. Further suppression of SRP19 expression is lethal only in cancer cells that harbour loss of SRP19.

Visit Associate Professor Rosenbluh's Monash research profile to see a full listing of current projects.

Research activities

  • Development of PROTACS as new tool to target proteins.
  • High throughput RNA-Seq following CRISPR mediated perturbation of gene expression.
  • Systematic studies of circular RNA.

Techniques/expertise

  • High throughput genetic screens (CRISPR, ORF or RNAi)
  • Cell biology
  • Cancer biology
  • Molecular Biology
  • High throughput sequencing.

Disease models

  • Cancer cell lines
  • Mouse models
  • Primary human cancer models

Collaborations

We collaborate with many scientists and research organisations around the world. Some of our more significant national and international collaborators are listed below. Click on the map to see the details for each of these collaborators (dive into specific publications and outputs by clicking on the dots).

  • Prof. Georgia Chenevix-Trench, QIMR, Brisbane
  • A/Prof. Stacy Edwards, QIMR, Brisbane
  • A/Prof. Juilet French, QIMR, Brisbane
  • Dr. Jonathan Beesly, QIMR, Brisbane
  • Prof. Patrick Tan, NUS-Duke, Singapore
  • Prof. Greg Goodall, Centre Cancer Biology, Adelaide
  • Prof. José Polo, Monash University
  • A/Prof. Max Cryle, Monash University
  • Prof. Eva Segelov, Monash Health
  • Prof. Melissa Southey, Monash University
  • A/Prof. Ron Firestein, Hudson Institute of Medical Research
  • A/Prof. Jianging Song, Monash University
  • Prof. Jill Mesirov, University of California, San Diego, USA
  • Prof. Pablo Tamayo, University of California, San Diego, USA
  • Dr. Jong Wook (William) Kim, University of California, San Diego, USA

Student research projects

The Rosenbluh Lab offers a variety of Honours, Masters and PhD projects for students interested in joining our group. There are also a number of short-term research opportunities available. You are encouraged to contact A/ Prof Joseph (Sefi) Rosenbluh regarding potential projects that align with the presented research themes.