I am Alessandro, physicist trained in biophysics and biology. My track record will tell you that my research is quite eclectic as I have published work across various disciplines, spanning information theory, sensor technologies, molecular biology and cell biology. I love to tinker with technology, develop new algorithms and software and I am best known for these aspects of my work. However, the molecular mechanisms of disease (neurodegeneration, malaria and cancer) have been always the focus of my biophysical developments. The passion for science and technology can be even more rewarding when addressing problems whose solutions can have a high societal impact. Cancer biology is my passion since 2010, a field where I believe I can make an impact. Since 2017, I lead a team of scientists dedicated to transdisciplinary research aimed to enable a live single-cell systems biology of cellular decisions and applying these tools for a better understanding of carcinogenesis. In 2022, I moved to Brunel University London as a Lecturer in Bioscience.
After the unfortunate closure of the MRC Cancer Unit and the struggles of the pandemic, I moved my Cambridge laboratories to Brunel University London. I am now focusing on re-establishing funding streams and – with a bit of luck – I will build a new group in 2023. I wish to thank everyone in my team, for their resilience, their passion and for being such amazing colleagues in difficult times.
The KRAS dream-team (2019-2022)
Suzan Ber joined the team in January 2017 as a post-doctoral scientist, moving to my team from the Venkitaraman laboratory. Suzan works on KRAS signalling and KRAS-dependent phenotypes.
I obtained my BSc in Biology at Middle East Technical University (METU) in Ankara, Turkey where I also did my MSc in tissue engineering and Biomaterials. I worked on developing patterned collagen surfaces seeded with bone marrow derived cells for bone tissue regeneration. It was then when I developed an interest in stem cells, more precisely adult stem cells and their capability to differentiate/transdifferentiate to different lineages. During my PhD at University of Goettingen, Germany I studied the multilineage potential of bone marrow derived stem cells and shown that their differentiation capabilities can be exploited in vitro by growth factors and Tat-Nanog protein transduction and in vivo by targeting cells to tissues using CXCR4.
Suzan says: “I then worked at the Gurdon Institute in Cambridge as a post-doctoral scientist in Prof Azim Surani’s group on regulatory pathways involved in neural stem cell plasticity. We have shown that foetal neuronal stem cells undergo a dedifferentiation process mediated by EMT that broadens their differentiation potential to mesoderm and endoderm lineages. Cancer cell’s ability to dedifferentiate through EMT have attracted my interest in cancer biology and brought me closer to clinical research. Therefore, I worked with Dr Colin Watts on the characterization of heterogeneity in patient-derived glioblastoma cell lines where we have shown that different populations exhibit differential drug resistance. I then moved to the laboratory of Prof Ashok Venkitaraman working on a drug discovery project that lead to the development of a novel PLK1 protein-protein interaction inhibitor. I have characterised its mechanism of action and identified the vulnerability of KRAS mutant cancer cells.
I am now enjoying working together with a very enthusiastic and collaborative team on the understanding of the biology underpinning specific KRAS mutations. I am identifying mutant-dependent phenotypes aiming to identify mechanisms underlying tissue-specificity in KRAS-driven tumours and mutant-specific vulnerabilities that could aid patient stratification and disease management. Curiosity is what motivates me and drove me across different areas of biological research and keeps me going every time I face an obstacle.”
Where did Suzan go? In 2022, Suzan moved to the Babraham Institute as a Senior Scientist, working in the group of Dr Simon Cook in Cambridge.
Andrew Trinh joined the team in the autumn 2018 as a post-doctoral scientist leading the development of advanced biochemical imaging technologies and working on the characterization of KRAS signalling.
Andrew says: “I earned my bachelor’s degree in bioengineering from the University of California, San Diego in 2010. During this time, I gained experience in cellular and molecular biology techniques in Professor Shu Chien’s laboratory while studying the role of microRNA in the mechanotransduction of flow-induced shear forces on vascular endothelial cells. In addition, I joined Biogen Inc. during the final year of my undergraduate studies to investigate the mechanism of action of rituximab, an anti-CD20 monoclonal antibody used to treat certain cancers and autoimmune diseases.
Following my undergraduate studies, I decided to pursue more engineering-focused roles. One of these roles was at ACEA Biosciences Inc. where I was part of a multidisciplinary team that developed the NovoCyte Flow Cytometer. This experience encouraged me to pursue a graduate degree in order to help me one day lead my own team.
In 2013, I began my PhD with Dr. Michelle Digman in the Laboratory for Fluorescence Dynamics at the University of California, Irvine. During my PhD, I received a training fellowship with a focus on biophotonics from the National Science Foundation. I specialized in fluorescence lifetime imaging and its applications in studying tumour heterogeneity using genetically-encoded FRET biosensors and metabolic imaging of NAD(P)H autofluorescence.
After my PhD, I joined the Esposito Group in 2018 where I continue to research fluorescence lifetime imaging techniques. My projects are motivated by the goal of developing new tools to answer questions in cancer biology and include the development of wide-field imaging techniques and faster image acquisition methods.”
Where did Andrew go? In 2022, Andrew moved to the Sanger Institute as a staff scientist in Cambridge.
Omid Siddiqui joined the team in January 2020 as a post-doctoral scientist recruited by the CRUK-funded OncoLive initiative. Omid leads the development of light-sheet microscopy and imaging of organotypic cultures.
Omid says: “I thoroughly enjoyed my MSci Physics at Royal Holloway University of London. The fourth-year was particularly memorable as I got to quantify the size of forest fires using data from NASA’s Landsat satellites, demonstrated a novel way of creating a passive indoor positioning system using Wi-Fi, and made contributions to the quantum referenced platform which is used to define the Volt at the National Physical Laboratory. The underlying element to projects I had conducted up until then was sensing and detection and hence, I joined the Sensors Centre for Doctoral Training (CDT) at the University of Cambridge. It’s here where I discovered my interest in optics and biotechnology. In the first year of the CDT programme, we worked as a team and spent the summer building an optical projection tomography microscope, which we then used to obtain three-dimensional images of organoids and C. elegans.
Continuing the theme of optics and biotechnology, I embarked on a PhD journey in the Optofluidics, and Laser Analytics Lab (Cavendish Laboratory, and Chemical Engineering and Biotechnology, University of Cambridge), investigating the use of thermal and optical gradients in microfluidic environments to quantify binding kinetics of misfolded proteins. I then joined the Esposito Lab at the MRC Cancer Unit in early January of 2020 and am now very much immersed in the field of biochemistry and cancer biology. Using the bespoke lightsheet microscope that I am building, we will gain a better understanding of the decisions and interactions between normal and cancerous cells in organoids and three-dimensional cell cultures.”
Where did Omid go? In 2022, Omid moved to Illumina as Senior Scientists in Cambridge.
Pablo Oriol Valls joined the team in autumn 2016 as an MRC DTA funded PhD student working on single-cell KRAS signalling.
Pablo says: “I started University life in September 2011 at Surrey University where I eventually obtained a BSc in biochemistry. It is during this time where my interest in cancer sparked. I was particularly intrigued by cancer cells’ ability to adapt to challenging conditions by shifting their metabolism (the Warburg effect). This led me to choose my final year project in a cancer-relevant topic: Effects of overexpression and deficiency of alkyladenine DNA glycosylase – an enzyme involved in Base Excision Repair – on induction levels of cell cycle inhibitor p21. In the third year of my degree, I carried out a placement year at the University of Bonn in Germany, where I worked on the role of endogenous opioid peptides in obesity. Wishing to see a more direct impact on people of my work, I then embarked on a Masters of Clinical Research at Imperial College London in October 2015. Here, I studied the potential use of metabolomic profiling of epithelial ovarian cancer as a predictive biomarker of response and toxicity to anti-angiogenic chemotherapy. Thanks to this experience, I realised that even if closer to healthcare applications, biomedical research is a long-term game. Therefore, I re-embraced fundamental research and started my PhD on KRAS biology using cutting-edge technology. I study cell-to-cell variability in MAPK signalling and its potential synergy with genetic variability in carcinogenesis. I combine microfluidics, FRET-based sensors, optogenetics and custom-made software to control and monitor biochemical reactions in single living cells.”
Where did Pablo go? In 2021, Pablo started his new job at EORTC as Clinical Operations Manager in Brussels.
Khushali Patel joined the team in summer 2017 with an MRC DTP PhD studentship entitled “Mapping changes in cellular information transfer underlying cell-fate decisions triggered by oncogenes” in collaboration with the Hall lab.
Khushali says: “I completed my Bachelor’s degree in Biomedical Science from King’s College London in 2014. This was a very interdisciplinary degree course that allowed me to explore not only the more ‘traditional’ fields of science such as biochemistry, pharmacology and genetics but also others such as forensics, psychology and nutrition. At this point, I had no desire to do research in the future and welcomed this opportunity to study a broad range of subjects. By the end of my undergrad studies, I realised my interests laid more in the pharmaceutical sector and drug development, and I also became interested in business within the scientific field. Therefore, I then started my Master’s degree in Pharmaceutical Formulation and Entrepreneurship at University College London in 2015. I was split between the School of Pharmacy under the guidance of Dr Gareth Williams and the School of Management under Dr Susana Frazao Pinheiro and the aim of this degree was to integrate science and business and equip scientists with entrepreneurial skills. I undertook subjects such as biopharmaceuticals, nanomedicine and entrepreneurial marketing and finance. It was not until starting my mini lab-project that I started developing an interest in research. My project was based on using electrospraying to produce solid lipid nanoparticles for dermal delivery with the aim of improving treatment for vitiligo. I carried out characterisation studies using techniques such as X-ray diffraction, infrared spectroscopy and differential scanning calorimetry. Although very different from the techniques I use now for my PhD, it led to me developing an interest in research, ultimately within the field of cancer biology.
I am currently studying how different KRAS mutants rewire downstream signalling to evade cell death and alter cell fate decisions.”
Where did Khushali go? In 2022, Khusali started her new job as Principal Analyst at Sagentia Innovation in Cambridge.
Annie Howitt joined Dr Christian Frezza’s laboratory and our team in autumn 2018 in a joint project dedicated to investigate metabolic cell-to-cell variability in model of KRAS-driven oncogenesis and of mitochondrial dysfunction.
Annie says: “I obtained my Bachelor’s degree in Biochemistry from Imperial College London in 2018, which included a number of laboratory projects. After my first year of study, I learned the basics of molecular cloning in the Crisanti Lab at Imperial, whose objective was to engineer a sex bias in mosquitoes. In the third year of my studies, I completed a year in research placement in Paul Huang’s lab at the Institute of Cancer Research. In this project working alongside PhD student Simon Vyse, I focused on understanding functional pathway dependencies in intrinsic resistance to EGFR inhibitor therapies in non-small cell lung cancer. This involved developing a CRISPR interference platform to study synthetic lethal candidates. I took the opportunity in my final year of teaching to focus my studies on metabolic network engineering, cancer and glycobiology. Finally, as a 10-week project culminating in my undergraduate dissertation, I worked on the characterisation of the bovine innate immune system receptor, Dectin-1 in the laboratory of Professor Kurt Drickamer and Maureen Taylor. From these experiences, I focused my interest on biological networks, cancer biology and signalling.
Currently, I am a joint PhD student in both the Frezza and Esposito labs, investigating metabolic heterogeneity in KRAS mutant cancers with microscopy“
Where did Annie go? In 2022, Annie started her new job as Communities Officer at Sense about Science, in London.
Anna Clay joined our team in Autumn 2020 to work in collaboration with Dr Jacqui Shield at the MRC CU and Dr Simon Cook at the Babraham Institute on cell-t0-cell communication in KRAS-driven cancers.
Anna says: “I obtained my BSc in Biological Sciences from the University of Leeds in 2019. This course gave me a comprehensive foundation in molecular and cellular biology and allowed me to tailor my studies to immunology, cancer biology and virology modules. My final year research project involved the characterisation and development of oncolytic Adenoviruses designed for cancer treatment, which aligned with my interests in the area of novel therapeutic development for cancer treatment. During my degree, I undertook a 15 month placement at Covance, a global contract research organisation, investigating the metabolism of small molecules and biologics. Here I gained an understanding of the pipeline for drug development and experience in whole-body autoradiography, pharmacokinetic analysis and xenograft studies. This placement solidified my resolve to contribute to the process of therapeutic development, with a particular desire to focus on the cellular processes that lead to the identification of novel targets. After graduation in 2019 I moved to Cambridge where I worked on a CRUK Grand Challenge project led by Professor Sir Michael Stratton, titled “Mutographs of cancer”, which aims to identifying preventable causes of cancer. I was based in the laboratory of Dr David Kent and Dr Elisa Laurenti at the Cambridge Stem Cell Institute. My work focussed on characterising mutational signatures in haematopoietic stem and progenitor cells associated with exposure to specific carcinogens including:chemotherapeutic agents, tobacco smoke and aristolochic acid.
Having enjoyed the research environment at Cambridge I decided to further my passion for cancerexploration and sought a PhD and I am now studying the biochemical signalling in cancer cells, specifically the effects of KRAS mutations on cell decisions from a non-cell autonomous perspective.”
Where did Anna go? After the closure of the MRC Cancer Unit, Anna moved to Simon Cook’s laboratory at the Babraham Institute in Cambridge, and we still work together.
Shaliny Sothyratnam joined our team in the summer of 2021 thanks to the ERASMUS programme. Shaliny braved a pandemic and BREXIT to spend the summer with us studying heterogeneity in KRAS signalling.
Shaliny says: “I obtained my bachelor’s degree in Pharmaceutical Chemistry from the TH Cologne, University of Applied Sciences in Germany in 2020. During my bachelor’s I especially gained experience in molecular biology and cancer research. In my final year, I performed an internship at Henkel where I was able to deepen my knowledge about biochemistry, by testing and characterizing properties of enzymes and optimization of zymographic methods for protein analysis. Within the scope of my bachelor thesis, in the lab of Prof. Nicole Teusch in Osnabrueck, I studied the anti-inflammatory properties of different herbal extracts for the treatment of inflammatory skin diseases such as psoriasis, rosacea and acne vulgaris. Furthermore, I examined novel purine nucleoside derivatives as drug candidates for the treatment of PDAC in 3D-spheroid cell models. After I finished my bachelor’s degree, I performed an internship at EVORION in Muenster working on single-cell analysis using microfluidic devices. I started my master’s degree in Immunobiology in October 2020. During my studies, I was able to expand my knowledge about the role of the immune system in different diseases and cellular heterogeneity.
In July 2021, I joined the Esposito group at the MRC Cancer Unit to perform a summer internship as part of my master’s degree. I am studying the cellular heterogeneity in MAPK signalling within different KRAS mutants using phosphoflow and work on the development of different FRET sensors for the metabolic analysis of single cells using Fluorescence Lifetime Imaging Microscopy (FLIM).”
Callum Campbell rejoined the team as a post-doctoral scientist in autumn 2019. Callum is leading our efforts on the study of cell fate decisions
Xiaoyu Wang | PhD student (CCIMI) in collaboration with Carola-Bibiane Schonlieb at DAMPT and Stefanie Reichelt at CI. Xiaoyu a mathematician working on machine learning and biochemical multiplexing during a first-year rotation in 2019.
Xianglong Tan | PhD student (SensorCDT) in collaboration with Carola-Bibiane Schonlien at DAMPT. Xianglong is an engineer who worked on machine learning and lineage tracing ina SensorCDT mini-project in 2019.
Camilla Cucinotta (2019)
Kayla Butkow (2020)
Moving on to KRAS signalling (2017-2018),
towards an independent group
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 University of Edinburgh and the University of Amsterdam, respectively. John is shadowing Callum, completing linage tracing experiments in the presence of DNA damage and working on cloning of FRET sensors and optogenetics tools for ERK and KRAS signalling. Tom is working on a FRET sensor and optogenetic tools for PI3K signalling and comparison of different KRAS mutants together with Pablo and Suzan.
In late summer, Khushali Patel joined us from UCL on a MRC DTP studentship in collaboration with Ben Hall (MRC Cancer Unit) and AbCam. Khushali is working on the understanding of how KRAS mutations rewire signalling pathways during early oncogenesis, hoping to discover novel mechanisms that could be leveraged 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 working on FRET sensors and optogenetic tools related to KRAS signalling pathways. Pablo is using single-cell imaging techniques to characterize the role of non-genetic and genetic heterogeneity in KRAS driven early oncogenesis.
In January 2017, Suzan Ber moved across teams within the Venkitaraman lab to my team (embedded in the Director’s group) as a post-doctoral scientist. Suzan earlier 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 transduction 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) as part of the Venkitaraman lab.
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.