I joined the Venkitaraman laboratory with an EPSRC fellowship in late 2009 thanks to the will of the Director Ashok Venkitaraman to employ the technologies I was developing in a different field, to cancer biology. Ashok’s support, thus, has been invaluable to transform my research project into a broader research programme dedicated to the study of cancer.
We are located at the Hutchison/MRC Research Centre within the MRC Cancer Unit now a department of the University of Cambridge. The mission of the Unit is to improve our understanding of the earliest steps in tumorigenesis and translate this into clinical practice by developing new diagnostic and prognostic tests, and therapeutic interventions.
Suzan Ber | post-doctoral scientist, biologist working on KRAS signalling and KRAS-dependent phenotypes
Andrew Trinh | post-doctoral scientist, engineer working on advanced biochemical imaging technologies
Pablo Oriol Valls | 3rd year PhD student (MRC DTA), biologist working on our FRET multiplexing platform and non-genetic heterogeneity in KRAS signalling
Khushali Patel | 2nd year PhD student (MRC DTP) in collaboration with Ben Hall group at the MRC CU, biologist working on KRAS signaling
Annie Howitt | 1st year PhD student (MRC DTA) in collaboration with Christian Frezza group at the MRC CU, biologist working on KRAS and cell metabolism
Xiaoyou Wang | 1st year PhD student (CCIMI) in collaboration with Carola-Bibiane Schonlieb at DAMPT and Stefanie Reichelt at CI, mathematician working on machine learning and biochemical multiplexing.
Xianglong Tan | MPhil student (SensorCDT) in collaboration wih Carola-Bibiane Schonlien at DAMT, engineer working on machine learning and lineage tracing
Moving on to KRAS signalling (2017-2018)
From the left: Suzan Ber, John Saganty, Pablo Oriol Valls, Tom Schoufour, Maximilian Fries, Alessandro Esposito, Callum Campbell, Kalina Haas and Khushali Patel.
2017 is the year of turn-over of people and projects, with our work increasingly focusing on KRAS signaling in the context of genetic and non-genetic heterogeneity.
In autumn, John Saganty and Tom Schoufour joined us as master students from the The University of Edinburgh and the University of Amsterdam, respectevly. John is shadowing Callum, compleiting linage tracing experiments in the presence of DNA damage and working on cloning of FRET sensors and optogenetics tools for ERK and KRAS signaling. Tom is working on a FRET sensor and optogenetic tools for PI3K signaling and comparison of different KRAS mutants together with Pablo and Suzan.
In late summer, Khushali Patel joined us from UCL on a MRC DTP stutendship in collaboration with Ben Hall (MRC Cancer Unit) and AbCam. Khushali is working on understanding how KRAS mutations rewire signaling pathways during early oncogenesis, hoping to discover novel mechanisms that could be levaraged for therapeutic or diagnostic purposes.
In late 2016, Pablo Oriol Valls joined us after a Master at Imperial College London to take over the KRAS projects started by Max earlier on. Pablo is wokring on FRET sensors and optogenetic tools related to KRAS signaling pathways. Pablo is using single cell imaging techniques to characterize the role of non-genetic and genetic heterogeneity in KRAS driven early oncogenesis.
In later 2016, Suzan Ber moved across teams within the Venkitaraman lab as post-doctoral scientist. Suzan earleir work focussed on PLK1 and KRAS sensitization. Now, Suzan is working to identify differences in KRAS-driven tumours, focusing on mutation-specific phenotypes and their mechanistic dependency on KRAS signal transtduction networks.
Callum and Kalina have continued their work on DNA damage to prepare their manuscripts.
The DNA damage checkpoint era (2014-2017)
During these years we still focused on assay development quite heavily, but we significantly increased our efforts on applications. Although not part of my team, I had a very successful collaboration with Hongqing Liang, PhD student in the Venkitaraman lab who influenced later projects and helped in gearing up other work. Hongqing discovered that the DNA damage checkpoint is very heterogeneous and proposed that the DNA damage checkpoint does not have a fixed threshold of DNA damage that can be sensed. Rather, DNA damage regulates the accumulation of pro-mitotic signals that will eventually result in the transition to mitosis, that may happen before the resolution of DNA damage.
In mid-2013, Maximilian Fries rejoined my team as a vacation student leading to the start of his PhD with a prestigious Gates Foundation studentship. Max joined from Wuerzburg after his earlier stint in our lab as a master student. I owe a lot to Max as he did not think to do a PhD in Cambridge, but he liked our research so much that committed the good part of 5 years of his life to working with us. He worked on the development of a unique FRET multiplexing platform, establishing the first optogenetics tools in the lab and set up the first KRAS related project with me. Max worked on many projects, but the main work he has done, aside from development of new techniques, is the understading of how Caspases are activated during the DNA damage response leading to apoptosis or necrosis (unpublsihed work). Max’s love for science, activism and policy lead him to go back to Germany at the end of 2017, joining an European MP for the Green Party as head of staff in a local constituency.
In a similar period, Siddharth De joined the group from the National Institute of Immunology, New Delhi after a short stint in industry at Daiichi-Sankio. Siddharth studied the dynamic response of MAPK and p53 signaling in response to the DNA damage response. Siddharth used a combination of standard tools, with FRET sensors for ERK activity and light inducible RAF kinase. Siddharth has shown (unpublished work) that opposing signals, pro-arrest and pro-survival, competes to set fidelity and timing of the DNA damage checkpoint. Siddharth left in 2017 to work at the Centre for Chemical Biology and Therapeutics, inStem, Bangalore in a laboratory lead by Prof. Ashok Venkitaraman with Dr Gayathri Sadasivam.
In October 2013, Callum Campbell was awarded a very competitive studentship sponsored by the Cambridge Cancer Centre – CRUK. Callum worked on novel tools (biochemical sensors and optogenetic tools) to study cehckopint signalling. The main research project he lead was the understading of checkpoint signaling, particularly in relation to those cells that fail to repair DNA damage and carry DNA damage through mitosis. Callum became an expert molecular biologist and coder, developped FUCCI-based cell lines and built an invaluable database of cell lineages of cell that had experienced DNA damage.
In early 2014, Kalina Haas, a physicist trained in super-resolution microsocpy coming from the Choquet’s group in Bordeaux joined us to complete what eventually formed the first team of people who worked with me on a cohesive research programme. Kalina worked on two projects: i) using super-resolution microscopy Kalina described the ultrastructure of DNA damage repair foci during homologous recombination, identifying a novel role for the C-terminal region of BRCA2 and ii) developed novel mathematical tools for the unmixing of several biochemical reactions in living cells. Kalina left in January 2017 to the Hersen’s Lab in Paris.
We also hosted Harveer Dev for a short stint on tumour imaging and Maria Zagorulya to set up modular response analysis in the lab.
Building a team (2012-2013)
From the left: Maximilian Fries, Emma Key Richardson, Marina Popleteeva, Alessandro Esposito and Siddharth De.
Marina Popleteeva joined my team in 2012-2013. Marina is a physicist, who was coming from the group of David Stoppa at the Fondazione Bruno Kessler. At the enf of my PhD, I contacted David hopeing to start new developments for spectrally resolved FLIM. It took many years to design, test and integrate technologies across the two groups, but eventually we were succesful. Marina was instrumental in adapting and characterizing these new solid-state technologies including development of software and algorithms. Marina left in 2013 to rejoin her family in Luxemburg where she went back to study and retrained in Systems Biology.
During a gap year, waiting to recruit Max back to build the FRET mutliplexing platform we had started to develop, Emma Key Richardson started to work with me as a Research Assistant, helping in the cloning of new optogenetics tools. Emma had the arduous task to clone and characterize far red FRET pairs that remained elusive for a long time. Emma then left to follow her dream to start a PhD, right next door in the newly established group of Sakari Vanharanta working on the study of metastatic cancer.
Siddharth De and Maximilian Fries then joined the group, but more about them in the next section.
Early times (2009-2011)
My initial years at the MRC Cancer Unit have been dedicated to developing technologies, mathematics and software for a new generation microscopes dedicated to single cell biochemistry. These development started with the aim to characterizing cell biochemistry during tumorigenesis and the heterogeneity underlying cellular responses that is responsible for the reduced efficacy of many therapies.
The project goals were ambitious and, therefore, a number of people within the Venkitaraman laboratory helped me in this period to kick-start the substantial molecular biology efforts that were needed to create the novel assays we were planning: Bryn Hardwick, Meredith Roberts-Thomson, David Perera, Helen Robinson and Pooja Sharma.
In these years, two master students pushed these efforts in a more systematic manner, Maximilian Fries and Henning Falk. Max successfully cloned and tested a large part of a biochemical multiplexing platform and continued his work with me during his later doctoral studies.