Meetings & Events
TransPot 2nd Training course
Systems biology/medicine and 'omics' technology
Biomedical Research Foundation of the Acadmey of Athens (BRFAA), Athens. 2nd - 4th October 2018
Training Course report by Marouane Kdadra (ESR 6), numares HEALTH, Germany
Training Course Description
The second TransPot training course took place from 2 to 4 October at the Biomedical Research Foundation of the Academy of Athens (BRFAA). The course was attended by TransPot's members and partners with the focus on Systems biology/medicine and 'omics´ technology. The main objective of the training course was to provide the ESRs with skill sets that will allow them to operate in multi-disciplinary programs in both today's academic and non-academic sectors.
The program was rich, very diverse and dynamic. It covered the basics of multi-omics technology and their utility in multiple use cases such as biomarker discovery, signaling networks and computational modeling. In addition, other courses from different disciplines were also part of the training (statistics, computational modeling) which were interesting in such a way that the ESRs could understand the multi-disciplinary aspects of their own projects and the implications of other tools and sciences in achieving their objectives based on omics data.
Furthermore, a career development session was also held in order to answer the ESR's questions relative to the outcome of their projects and the possible career options that they could have. A hands-on experiment workshop was also part of the program where the ESRs had the chance to see how pathway enrichment analysis is performed with Cytoscape (basics only). The course also contained a complimentary skills session that was about grant writing: It helped the ESRs to know about the possible funding options for their future projects and how to properly apply for grants. The training was concluded by a proteomics lab visit at the host institution (BRFAA) where we got an overview on the work of the lab and the devices used for the measurements and their functioning principles.
The program contained also an ESR progress updates session which was exclusive to PIs and ESRs and during which the latter gave a fifteen minute presentation of their projects and the results that they have achieved so far. Each presentation was followed by questions from the PIs and ESRs that led to very interesting discussions. It was an opportunity for every member of the team not only to know the progress of the other projects and the nature of their work, but also to get advice and different perspectives from other team members.
Networking was also one of the main focuses of the training all along, either during coffee breaks or lunch time. A consortium meal was also organized for this particular purpose where ESRs, PIs and some TransPot's partners had a dinner together in a friendly environment.
· The training was a great opportunity for the ESRs to have an overview on the "omics" technology and how the latter is important in the biomarker discovery and the modeling of the complex biological systems.
· The talks were diverse and complementary in such a way that the ESRs could understand the possibilities that are existing in the field and how they are related to their specific projects.
· Other talks were also of great importance to the ESR's career options in both academic and non-academic fields.
· The ESRs had the opportunity to present their work to the other TransPot members (PIs and ESRs) which permitted them to practice their presentation skills as well as sharing their results with the other members.
· The Training course enabled the TransPot members to develop their network and discuss mutual interests in person.
TransPot 1st Training course
Molecular mechanisms and clinical aspects of Prostate Cancer
Erasmus Medical Centre, Rotterdam. 17th - 19th January 2018
Training Course report by Syeda Afshan (ESR4), University of Turku, Finland
Details of training course
Lectures and discussion: The presentations from scientists and clinicians working on various fields of cancer biology were informative. The program was well organized and gave us an idea of the various fields of cancer, particularly PCa, which are explored in research today.
The scientific talks and discussions included the following:
• Starting with the basics of molecular pathways in PCa, function of androgen receptor, role of non-coding RNA and vasculature in PCa
• Molecular and immunological biomarkers employed for diagnosis of PCa
• The screening outcomes and methods used for risk stratification of PCa (we were introduced to the interesting and reliable risk calculator, which is being used in The Netherlands)
• Research on in-vitro 3D cultures, ex-vivo and in-vivo preclinical models of metastases as a heterogeneous and representative model for understanding the interaction between tumor cells and tumor microenvironment, testing the response of compounds against PCa and their possible application in personalized medicine
• The various established and upcoming methods used for diagnosis and therapy
• If and when the patient becomes resistant to androgen deprivation therapy then the management and treatment of castration resistant prostate cancer (CRPC) was described
• Using various modern tools and technologies like RNA- sequencing, live cell imaging, high content screening to help the research community to better analyse and interpret the data
• Finally, the journey of a potential anti-cancer compound from being a hit in high throughput screening to a lead and finally a drug and its commercialization.
Lab tour: We had a lab tour for one hour on the second day of training. It was not just refreshing but also informative. We got an opportunity to see the facilities and techniques employed for the cell culture and processing of tissue from patient derived xenografts. We had an interactive chat with the lab members about their well-maintained cell culture rooms, workspace for histopathology, automation and advanced microscopy for imaging and analysis.
Group activity: During the second part of Day 1 of the training, we had an interesting and enjoyable 'presentation and communication skills' workshop headed by Jennie Wilde. Each of the nine ESRs gave a brief presentation on our research work, its significance and our aspirations. Our presentations were video recorded and played back for us to see how we performed. This group activity was fantastic, as we received feedback from all attending the session about our delivery of the content, clarity of thought, body language and how to improve on our presentation skills. I found this to be an effective way to improve not just our communication skills, but to realize how to deliver the 'what', 'why' and 'how' of our research to make it effective and captivating to the audience. Furthermore, this helped all of us get an idea about the research topics of our fellow ESRs and to think about potential collaborations with them during our secondments and to seek advice on some topics of our research.
At the end of the training course, we could picture a pipeline (Research-Preclinical-Clinical) of steps from laboratory to clinic. Additionally, it also created awareness about the unanswered questions in PCa diagnosis and treatment, the laboratories which would be ideal for our secondments, clarity of thought and delivery of an effective presentation and the various career options which are available after achieving our doctorates,. Overall, it motivated us to reach our goals, keep an open mind and have keen observation during our doctoral training.
Training Course report by Rafael Sanchez Martinez (ESR1), University of Glasgow, UK
The TransPot first training course was a great start to our future work on prostate cancer (PC). It provided us with a nice overview of all the work that is being done on prostate cancer at every level: Laboratory and clinic, diagnostic and treatment, feedback to research. This was very useful for us, as it introduced all the fields involved in prostate cancer research, something we need to be aware of since each one of us works in our own areas. Having a clear picture of all the parts involved will help us develop our own research better by making us aware of the context. It was also reinforced and complemented our own knowledge in the areas we might be working on.
To educate us in the clinical aspect of prostate cancer, we had talks about several steps of the dealing with prostate cancer at that level:
- The screening of PC: How does it work, its caveats, and how should we aim to improve it.
- The pathology of PC: Description of the Gleason method of scoring, one of the most recognised and well known methods of PC progression evaluation. We learnt what it means but also its possible pitfalls.
- Genetic biomarkers: How mutations in cancer cells can help us follow its progression as well as guide our approach to its treatment.
- PC from an urologist perspective: Since we mostly work in laboratories, this talk was really useful to see how clinicians see and tackle prostate cancer, which gives us perspective on the way we deal with it as scientists.
- Management of castration resistant prostate cancer: The appearance of tumours resistant to androgen deprivation is a staple of PC treatment and progression. This talk provided a nice overview of the current knowledge of the issue and how to deal with it.
- Researcher's perspective: This talk presented a nice array of in vitro PC models derived from patients, remarking on the importance of having the laboratory results be as faithful to the clinical results as possible.
- PC overview and evolution: To deal with PC and any cancer, we have to understand that the malignancy is a changing and evolving issue we cannot treat as a single entity.
There are many ways to approach the study of prostate cancer in the laboratory, and all of them are needed, since a complex disease as this requires a deep understanding of all its elements. To provide us with a broad knowledge of how this malignancy is studied, scientists delivered very interesting talks about their own work on prostate cancer:
- Molecular pathways of PC growth: How the PC cells have the ability to grow in an aberrant way and under unfavourable circumstances such as drug treatment. It is very important to know the signalling pathways involved in prostate cancer because the cells rely on them making them a solid target for therapy.
- Targeted therapies: How to operate on a single known gene, protein or agent promoter of prostate cancer.
- Tumour-host interactions: PC cells communicate with cells in the tumour microenvironment – this can be both pro- and anti-tumourigenic. The immune system plays a great role in the development of the disease and is something to always be aware of.
- Non-Coding RNA: The role of this RNA is not entirely known in general, and its study on prostate cancer has yielded interesting results making it a field of interest.
- Targeting vasculature in the endothelial cells: The blood supply of the tumour not only is important for its growth and survival, but also for drugs to reach it. How to increase blood-borne drug delivery in the clinic based on laboratory results, a nice example of the bench to clinic philosophy.
- Immune targets for therapy: Introduction to the concept of using the immune system as a fighting agent of cancer, activating its anti-tumorigenic effects.
- Preclinical models of metastasis: Provided a great explanation of a very clever experiment design to study how metastasis work in prostate cancer, with the use of colour marked cells to track the clonal origin of metastatic populations.
- Extracellular vesicles and PC: Exosomes are a recently opened field and their value as prediction markers is being studied.
- Organoids from circulating tumour cells: Study of the use of tumour cells that can be found in the blood to develop an in vitro model that matches the patient.
- Ex-vivo prostate cancer patient derived xenograft system: Means of in vitro culturing of a tumour sample directly obtained from the patient to use as a model for personalised treatment.
- Proteogenomics: How integration of different "omics" technologies can lead to the development of stronger in silico models.
- Quantitative live cell imaging and high content screening: What possibilities this technique can bring to PC research.
A couple of final talks improved our understanding of concepts that might be outside our range of action, but play an important role on research and treatment of prostate cancer and truly bind research to actual clinical action:
- Bench to bedside: Examples of one of if not the most important aspect of cancer research; the ability to produce results that lead to actual improvements in clinical treatment of the malignancy.
- Drug discovery and commercialisation: How the process of developing a drug works, from the initial laboratory work until it is produced and can be used as a treatment.
Apart from that, we received a training session on presentation skills, since communication of our research is an integral part of our life as scientists and can open the doors for collaborations and other ways to improve our work and make the most out of it.
We also enjoyed a couple of sessions where we could get to know each other and our work, something that will surely push us towards collaboration and greatly improve our experience in the TransPot network.
In conclusion, I feel it was a great start for us, building the foundations of our scientific knowledge on prostate cancer as well as the approach to our own work. I also leave the meeting with an enthusiastic feeling about the possibilities that this network will grant us and the work we will produce.
TransPot Kick-off Meeting
University of Glasgow. 5th - 6th July 2017
This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 721746