Bioinformatics Seminar
Time:
Venue: Na
27 September 2016
NaExtracting cellular hierarchy from high-dimension single cell data using SPADE and tSNE
Charis TehWEHI Molecular Genetics of Cancer Division
Targeting the molecular machinery of cell death can kill a broad range of cancer cells. Pioneering work at the WEHI ; collaborating with the pharmaceutical companies Genentech and AbbVie ; has led to the development of BH3 mimetic drugs such as ABT-737 and ABT-199.The initial success in the BH3 mimetic trials is promising but there are still aspects of the targeting that are poorly understood. How does treatment with BH3 mimetics alter the cancer cells? Do different clones of cancer cells present with different resistance or sensitivities to the durgs? Would targeting different combinations of apoptotic proteins result in a more effective cancer therapy? Answering these questions has been hampered by the lack of tools to simultaneously visualize the complete profile or signature of all apoptotic proteins in a single cell.
We utilized a new cutting-edge technology to deeply profile the survival and death switches in single cells isolated from healthy blood donors and cancer patients. The technology ; called mass cytometer (CyTOF) ; provides new insights to complex biological systems by allowing high-throughput detection of up to 43 different characteristics on a single cell ; more than five times the amount generated by its predecessor technology. Each protein-of-interest is tagged with a series of rare earth elements/metals (e.g. lanthanides) ; which are attached ; via metal-chelator coupling reagents ; to antibodies that can bind to proteins-of-interest in single cells. Cells that are labeled by incubation in a cocktail of different metal-tagged antibodies are then passed through the CyTOF instrument ; where they are vaporized at 5500K. The rare element tags are ionized and then quantified by time-of-flight mass spectrometry. Using computational tools such as SPADE and tSNE ; we aim to build a systems-level view of the regulation of apoptosis to reveal the differences between cancer cells that sensitive/resistant to treatment and provide clues about potential effective combination therapies.