If you discover in science something new, perhaps even something that goes against the mainstream, you could change other people’s views about how things work. And that is what Petr Beneš and his team from the Faculty of Science of Masaryk University, whose Laboratory of Cell Differentiation is part of NICR, have achieved. In the course of more than twenty years of studying the c-Myb protein, which was long considered to be an oncogene, they discovered to their great surprise that during some stages of carcinogenesis, it can function as a suppressor. In other words, they found that the function of this protein is crucially affected by the timing of its expression. ‘For me personally, this story shows that science is also about the courage to doubt ingrained convictions, and that unexpected results often lead to progress in our understanding of the biology of tumours’, says Petr Beneš.
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When did you decide to focus your professional and scientific interest on the interior of cells? Where did you gather experience and who was the greatest source of inspiration for you?
Already during my studies of molecular biology at Masaryk university I was namely attracted to subjects that dealt with organisms function at the cellular and molecular level. In contrast to more descriptive or systematic areas of science, I was fascinated by the idea of ‘exploring the depths’, by understanding how things really work. In this respect, I was especially influenced by lectures of Professors Šmarda and Doškař. They awoke this interest in me and then developed it further. During my doctoral studies, I focused on the genetic risk factors of coronary artery disease. This research was interesting but mostly based on association studies and rather routine analyses; it lacked the deeper investigation of the mechanisms as such. This was when I have fully realised that what I really want to explore is the ‘interior’ of cells, what determines their behaviour and their fate.
This motivation led me to a postdoc stay in the United States, where I started focusing on the experimental study of tumour cells and the mechanisms that affect their properties. After coming back to Czechia, I had the opportunity to continue this work thanks to Professor Šmarda, who offered me a position in his research team. The study of cellular mechanisms formed the foundation of research in his group, and at the same time, this position also allowed me to engage in teaching, which is something I find both interesting and fulfilling. It naturally brought things together: deep and meaningful research and the opportunity to share knowledge further.
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Aside from tumour biology, your laboratory is also engaged in the study of developmental processes. Are there any overlaps between these two areas? Do these processes have something in common in terms of molecular mechanisms?
Yes, developmental processes and carcinogenesis are closely linked, which is why it is useful to study them in conjunction. Many molecular pathways which are active during embryogenesis are re-activated in tumour cells. But while in embryogenesis these processes are strictly regulated in terms of timing and spatial organisation, in tumours they become deregulated, which contributes to the emergence of tumours and their aggressive behaviour. Developmental biology thus often studies the same cellular processes as tumour biology does, such as the regulation of gene expression, cell proliferation, differentiation, migration, plasticity, or interaction of cells with their surroundings. The study of development can often help us better understand how these processes function in a normal context, and thus also find out why tumours arise and what determines their properties.
In our laboratory, the study of developmental processes is mainly the domain of Jirka Kohoutek, who investigates the role of cyclin-dependent kinases in embryonic development and in certain types of tumours. We also have a long-term collaboration with Professor Eva Matalová: we jointly study the molecular mechanisms of bone development. These approaches enable us to see cell regulation from different perspectives – and it often turns out that findings coming from the study of the organismal development can be very effectively applied to cancer research as well.
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How challenging is it to experimentally validate bioinformatic analyses that suggest prognostic or therapeutic relevance of specific signaling pathways? Is there a sufficient time and resources to carry out such research in the Czech Republic?
Nowadays, we all have access to extensive public databases with transcriptomic, proteomic, and clinical data of patients with various types of tumours. These data can help us identify genes and proteins whose production is altered in tumour cells compared to healthy cells, but also those whose expression correlates with clinically relevant phenotypes, for instance with metastatic potential, therapy resistance, or prognosis. Validation of bioinformatic analyses is subsequently the key step that decides whether a given hypothesis has a real biological or clinical significance.
In our team, bioinformatic analyses are the domain of Lucie Knopfová and thanks to her, we always have in our sights new genes whose relevance to cancerous processes we attempt to validate. The process of validation is naturally time-consuming and experimentally demanding. Ideally, it includes work with various model systems including experiments in vivo in mice, since each model has its limitations. This combination of approaches enables us to verify hypotheses in various biological contexts. When done properly, validation usually takes years. It is moreover financially demanding and, in the Czech environment, success rate in grant competitions is relatively low. That is why we need to actively look for financial resources from all kinds of different available sources. On top of that, the often lengthy peer-review process in scientific journals can further prolong the process.
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Stromal and other non-cancerous cells are a significant part of the tumour microenvironment that supports tumour growth, metastasis formation, and the development of therapy resistance.. How does your laboratory contribute to a better understanding of their function and signaling? What methods do you use to study the interactions between tumour and non-tumour cells?
In recent years, the impact of tumour microenvironment on the behaviour of tumour cells has been intensively studied. It turns out that tumour microenvironment plays a key role in the regulation of tumour growth, in their ability to metastasise, and in the development of therapeutic resistance. It is therefore not surprising that many therapeutic approaches which target various components of the microenvironment with the aim of increasing the effectiveness of antitumour treatment are being clinically tested and, in some cases, already used.
Our laboratory has been, for some years, studying interactions between tumour cells and non-tumour cells in the process of metastasis, where the metastasising cells are exposed to various environments and interact with a wide range of cell types. Recently, we have expanded our focus to include the study of interactions between tumour cells and the microbiome, because it turns out that microbiome, too, can decisively influence their behaviour. Aside from cell interactions, we also study the specific conditions in the tumour microenvironment, such as acidosis or hypoxia. These factors have a strong impact not only on processes within the tumour cells but also on their interaction with the environment. In our team, experiments that investigate interactions between tumour cells and the microenvironment are mainly the domain of Jarka Navrátilová. Methodologically speaking, we use various co-cultivations systems, both classical 2D cultures and advanced 3D models, which resemble the spatial organisation of a tumour more closely. We also work with organotypic cultures, which enable us to study interactions in an authentic environment. Irreplaceable are experiments on mice, where one can use genetically modified lines with inhibition or depletion of particular cell types and see how it changes the growth of a tumour or its ability to metastasise.
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The international Journal Biological Research had published this summer an article from your research group describing the regulation of fascin-1 activity in the formation of actin bundles via tropomyosin isoforms encoded by the TPM2 gene.. Could you describe for us in more detail the results and their potential therapeutic relevance?
This study was conducted in collaboration with the research team of Professor Joanna Moraczewska from Kazimierz Wielki University in Bydgoszcz, Poland. Based on a bioinformatic analysis, we have noticed that in osteosarcomas, malignant metastatic bone tumours, the expression of the TPM2 gene, which encodes several isoforms of tropomyosin 2, is often reduced. This led us to ask why it is so and what role do these isoforms play in the regulation of metastatic activity of tumour cells. Tropomyosins are proteins which regulate the dynamics of actin cytoskeleton by influencing interactions between actin and other proteins. Meanwhile, the dynamics of the cytoskeleton influences various properties of the cells, including their migration ability and invasive growth. We have therefore joined forces with Professor Moraczewska, who has been studying functional interactions between proteins and actin for some years, and together we succeeded with a grant application at the Czech Science Foundation. The published article is the first result of this project.
In short, we have shown that isoforms of tropomyosin 2 influence the interaction of another important protein, fascin, with actin. Fascin is of key importance in the formation of strong actin bundles, which are crucial for migrating cells. Not surprisingly, fascin production is thus in metastasising tumours often elevated. Our results suggest that reduced TPM2 expression may enhance the interaction between fascin and actin, thereby promoting cancer cell migration and invasiveness – ultimately contributing to metastasis formation.
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Which other findings from your research group would you consider more or less ground-breaking?
Honestly, I value all the results achieved in our laboratory – every one of them was based on strong effort of the entire team. Experimental work is full of unexpected challenges and things often do not go according to plan. I believe that the ability to overcome these challenges and not give up in the face of partial failures is an essential part of scientific work. Of our numerous publications, however, I would like to highlight one story which shows that if you discover in science something new, even perhaps something that goes against the accepted mainstream, you can change other people’s ideas about how things function.
In our laboratory, we have been engaged in the study of the c-Myb protein for over twenty years. This protein has long been believed to be an oncogene, that is, a gene whose increased activity supports the emergence of tumours. Its oncogenic role has been described especially in leukaemias, which is why initially we focused on them as well. Later, however, we have noticed based on bioinformatic data that c-Myb is expressed at elevated levels also in breast and colon tumours. We expected that its behaviour would be similar to what was documented in leukaemias, that is, that it would support the growth of tumour cells. To our great surprise, however, we found that in some cases an increased expression of c-Myb can actually supress the tumour’s ability to form metastases, especially in the lungs. In collaboration with Professor Borsig from the Zurich University, we have then demonstrated that this effect is linked to c-Myb’s ability to regulate the production of proteins which influence the activity of endothelial and immune cells in the tumour/metastatic microenvironment. On top of that, we found that this protein’s role is crucially influenced by the timing of its expression: at different stages of carcinogenesis, it can function either as an oncogene or, on the contrary, as a suppressor.
I remember that when I first presented these results at an international conference, it led to a lively discussion. Many researchers were sceptical of the idea that an oncogene could have also the opposite role. Professor Harris from Oxford then concluded the debate by noting that if we accepted a black-and-white view of oncogenes, tumours would have to be much more mutually alike than they in fact are. And, indeed, since that time researchers have described more proteins with a dual function.
In my view, this story shows that science is also about having the courage to challenge ingrained preconceptions – and that ‘unexpected’ results often lead to progress in our understanding of the biology of tumours.
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How does your research team operate, not only on a professional but also personal level? Do you have a recipe for supporting creativity, communication, satisfaction, and interpersonal relationships? And how should one support young scientists?
Our team has several levels: aside from me, there are three junior/senior principal investigators who lead their own research directions, four doctoral students, and about six master’s students. Thanks to being part of a university, we have a natural influx of motivated students who want to be involved in research. After defending their thesis, our Ph.D. students go on to work at excellent institutions in the Czech Republic and abroad and we stay in touch with many of them. In some instances, we even consult their further research projects.
Regarding the functioning of a team, I have no ‘well-tried recipe’. I am trying to create an environment where people can work in an atmosphere of trust, openness, and mutual respect. I give people a lot of freedom – I am convinced that if they have space, they will not disappoint. And when something does not work out, no one is going to ‘bite their head off’. Failure is part of scientific work. What is important is to learn from it, pick oneself up, and continue. Team members can take part in various courses that develop both methodical and personal skills. Our Ph.D. students regularly take internships abroad, which is something I consider important for both their professional and personal growth.
I am happy to say that we have in our team several natural ‘powerhouses’ who take care of also the informal social aspect: they organise team buildings, birthday celebrations, and contribute to a good atmosphere in our lab. In my view, support of creativity and contentment is mainly about listening and giving people space to grow. And when that works out, one can see the formation of a team that works not only on a professional but also personal level.
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Your laboratory is part of NICR. Looking back…was it a good decision to join the project? Did cooperation within the consortium work out?
I am very grateful for the opportunity to join the NICR project. Naturally, one of the important advantages is the financial support of research, which enabled us to conduct demanding experiments and develop new directions. But no less important has been the creation of a platform that enables and facilitates interaction between among scientists working in cancer biology, whether in basic research or in a clinical context. Highly beneficial are also the annual meetings in Olomouc, which provide space for sharing results, establishment of new collaborations, and discussions about current challenges in the field.
Within NICR, we cooperate on numerous projects. Our close collaborator is Pavel Bouchal from the Department of Biochemistry of the Faculty of Science of Masaryk University: we use his expertise in proteomic analyses. We also cooperate with Karel Souček from the Institute of Biophysics of the CAS; we currently work together on a project supported by the Czech Science Foundation, which investigates the role of the Trop2 protein in the metastatic dissemination of tumours. I would also like to highlights our collaboration with several clinical departments, for instance with Michal Hendrych and Iva Staniczková Zambo from the First Institute of Pathology of the Faculty of Medicine of Masaryk University and St. Anne’s University Hospital in Brno, with Dagmar Adámková from Masaryk Memorial Cancer Institute, or with Peter Múdry from the Department of Paediatric Oncology of the Faculty of Medicine of Masaryk University and University Hospital Brno. Such cooperative efforts enable us to link basic research with clinical reality and get closer to applicable outputs that could have an impact on the diagnostics or treatment of cancer patients.
We have naturally also many cooperations outside NICR. Nowadays, almost all research is accomplished in collaboration with other teams – it cannot be done any other way. Each team brings its own specific expertise, so it’s efficient to entrust different parts of a project to specialists who truly master the relevant methods or research areas.. Such cooperation not only improves the quality of results but also helps us all to see the research questions from multiple angles and thus come up with more comprehensive answers. Moreover, it facilitates an open and critical discussion about projects as well as the results, which is of key importance for scientific research.
