#TheConorFoleyNeuroblastoma ResearchFoundation – Blog about neuroblastoma research

Ever wonder how scientists figure out a specific protein’s role in cancer?

Researchers use various methods, but I employ gene knockdown in my experiments. Basically, I use small RNA molecules that specifically target and degrade the mRNA of my gene of interest. This leads to a decrease in the corresponding protein levels, enabling me to observe the effects on neuroblastoma cell behaviour.

I feel a bit like Sherlock Holmes, you know? I’m selectively putting my suspect protein – the one I’m eyeing – under the spotlight to see how it’s pulling the strings on the cell’s behaviour. It’s like I’m in a cellular mystery, complete with a gene knockout magnifying glass 🔍🧬🕵

So, what I’ve been up to these past months is knocking down my protein and trying to find answers to the following questions:

Can neuroblastoma cells survive? And if not, how do they meet their demise? Do they go on a growth spree and start proliferating? Are they capable of migration? And here’s the twist – when my protein of interest takes a dip, do other proteins decide to change their expression levels?

The picture below can probably help you get an idea of what I’ve done so far. Do you see those brighter spots in Pictures A and B? Those are dead cells. Their number indicates the proportion of dead cells after a treatment. Picture A has just a few; the majority are healthy and well-spread cells. This is our negative control, a condition when we show neuroblastoma cells that have been transfected, but no gene knockdown happened. Transfection is the term for introducing small RNA molecules. Now, in Picture B, when we knocked down the protein, it caused the death of the cells, and you can clearly see that from all those many little bright spots.

We have found answers to many of the previous questions, but new questions have arisen, and we can’t wait to answer them!

Written by Federica Cottone

How things work in Science: Classifiers

For our next little series introducing a different thing in science and how it works every week, I decided to focus on classifiers. With artificial intelligence becoming more and more prominent in our daily lives as of late, I thought this would be a good lead into the explicitly science-focused topics to come. So, what is a classifier? How does it work? And why does it matter?

At their core, classifiers are algorithms designed to categorize input data into predefined classes or categories. They learn patterns and relationships from labelled training data to make predictions on new, unseen data.

Once features are extracted, identified and quantified from labelled or annotated input data, mathematical models are employed for pattern recognition and predictions.

These models can range from simple decision trees to complex neural networks, each with its own strengths and weaknesses.

Training these models is an iterative process. That means to produce one good classifier, lots of classifiers were created in the process: Every time the pattern recognition is run, the annotated data is categorised by the classifier and compared to the annotation class. Prediction errors are corrected, and performance is optimised. This whole process is one iteration. How many iterations are required for a well-trained classifier varies widely and is largely dependent on the input data and application. For my tissue classifiers, it took up to 20,000 iterations.

Classifiers use these models to categorise unseen data into categories the user-defined at the start. In the figure, you can see my annotated histological slides from which the classifier extracted patterns to then classify the rest of the slide and entirely unseen slides into tumour (red), stroma (green) and background (blue) classes.

From identifying fraudulent transactions, filtering out junk mail, targeted advertising, and facial recognition to unlock your phone or diagnosing diseases, classifiers play a vital role in automating decision-making processes and driving advancements across a wide range of industries. Keep your eyes peeled, and you can find more classifiers in action all around you.

Written by Ronja Struck

Women in Science: Rosalind Franklin

On a blog post series of Women in Science by a Cancer Bioengineering lab, you didn’t think you were going to get around reading about Rosalind Franklin, did you? In recent years, she finally started to receive the acknowledgement she is owed, placing her all the way up there in terms of famous scientists with Marie Curie and Albert Einstein.

As mentioned by Ellen last week, there were only ever 13 women to win the Nobel Prize in Physiology or Medicine. But in 1962, it was erroneously bestowed upon three men for the scientific breakthrough of a woman. This blog post would just as well fit into a true crime in science series.

All down to misogyny and a single piece of evidence: Photograph 51, an X-ray crystallography of the structure of DNA viewed perpendicular to the DNA fibre axis, revealing the double helix structure.

You will likely all remember James Watson and Francis Crick from biology classes in school. You were probably taught that they figured out the structure of DNA.

But at the same time, they worked together in Cambridge, Franklin was working together with her PhD student Raymond Gosling at Kings College in London. Forced to work alongside Maurice Wilkins, who did not take well to her confident, goal-oriented ways, which led her to criticise her well-respected peers and dared to interrupt and correct them.

Leading to her downfall in the race with Watson and Crick was that Franklin complied with her understanding of scientific ethics, and rather than rushing to publish her findings, she sought to verify them and replicate the findings in Photograph 51.

Betrayed by her colleague Wilkins after ample tensions over the years. He passes her priceless finding to the competition, allowing Watson and Crick to model the double helix, publish a breakthrough paper and relegate her to a methods paper in the same issue of the nature journal.

Tragically, her young death at 37 from ovarian cancer prevented her from witnessing the Nobel Prize being awarded for discoveries in the molecular structure of DNA four years later. Which in 1962 was not to be awarded posthumously. Instead, her reputation for years was dominated by the more than unflattering recollections in James Watson’s biography. The book clued the public into the crimes the three men committed. All the while tarnishing Franklin’s name, portraying wildly misogynistic images and downplaying her indisputable contribution to science. Only after society as a whole changed its views on women and misogyny did perceptions of Rosalind Franklin and James Watson finally get corrected.

Today, Rosalind Franklin’s legacy stands as a symbol of tenacity, intellect, and an unyielding spirit that will inspire generations to come. It is about time that science books get rewritten to remind us that those are the virtues we should hold in high regard. Rather than the yearning for glory and a legacy that we see in the pressure to publish, the chase of impact factors never intended to rank journals and scientists but as a tool for librarians and the impossible climb through academia, forcing impossible expectations on principal investigators to take on endless students and responsibilities. Let’s take this opportunity to refocus and make sure it’s the pursuit of knowledge and answering questions that drive science forward that determine our decisions.

Written by Ronja Struck

Knit-A-Thon 2023 Results

A wonderful day of knitting – Knit-A-Thon-2023 raised 913 euros. A massive thank you to everyone who stopped by and donated on the day and beyond. Every cent counts! The money was split evenly between our four chosen charities: The Conor Foley Neuroblastoma Research Foundation (CFNRF), Neuroblastoma UK (NBUK), Oscars Kids and Childhood Cancer Ireland (CCI). These charities were established and are run by parents, some of whom lost their children to cancer. They continue their children’s legacy, doing an amazing job of advocating for children with cancer and better funding for research and aftercare.

And a special thank you to Ciara’s mam Aggie for the amazing handmade raffle prizes (chromosomes, antibodies, cup holders and many more) and a Master class on the day! We thank Jenny Duffy (RCSI Events and Communications Coordinator) for her time crocheting with us and for us! Thanks to Anggie’s and Jenny’s skills, there were lots of mascots to win – and many of them collected already. We much appreciate the support from the RCSI Estates and Porters who looked after us on the day.

Go Raibh Maith Agat!!!

MANY THANKS FOR YOUR BIG HEARTS!!!

Knit-A-Thon 2023

We are the Cancer Bioengineering Group, and September is a very special month for us as it is Childhood Cancer Awareness Month. Childhood cancer is the 2^ndleading cause of death in children after accidents. Our group researches childhood cancer neuroblastoma, a cancer of immature nerve cells. Despite intensive multimodal treatment, as many as 1 in 5 children with aggressive neuroblastoma do not respond, and up to 50% of children that do respond experience disease recurrence with many metastatic tumours resistant to many drugs and more aggressive tumour behaviour that all too frequently results in death.

This is what we want to change! We believe that every child deserves a future, and our team of postgraduate researchers led by Dr Olga Piskareva is dedicated to strengthening our knowledge of this disease and identifying new potential ways to tackle it, as well as taking part in fundraising activities so our group and others can continue with this research.

On Tuesday, the 19^th of September, we are running a Knit-A-Thon using gold and purple yarn to mark childhood cancer and neuroblastoma, respectively. Our patterns are inspired by Neuroblastoma UK and Mr Google, indeed.

This year, we honour 4 charities that are doing an amazing job of advocating for children with cancer and better funding for research and aftercare. Therefore, the donations we receive will be split equally among The Conor Foley Neuroblastoma Research Foundation (CFNRF), Neuroblastoma UK (NBUK), Oscars Kids and Childhood Cancer Ireland (CCI). If you would like to get involved in the Knit-A-Thon and help us raise vital funds for childhood cancers, come along on the day and make a donation to these wonderful charities.

On the day, RCSI 123 SSG will #GoGold in support of this cause. Please come by to see the RCSI building lit up and share your pictures on social media with the hashtag #ChildhoodCancerAwarenessMonth to raise awareness.

Ready, Steady, Go!

Every year we manage to raise an amazing 1500-2000 euros by organising a new challenge. We are eager to surpass that target this year. All donations no matter how small are appreciated at GoFundMe.

Childhood Cancer Awareness Month 2023

Every September, we celebrate Childhood Cancer Awareness Month. This is a great opportunity to raise awareness about childhood cancer. Unfortunately, kids get cancer, too. While much research has been done to understand how cancer develops in adults, we still know very little about what exactly leads to cancer in children.

We are the Cancer BioEngineering Group led by Dr Olga Piskareva at the RCSI University of Medicine and Health Sciences. Our research focuses on neuroblastoma, an aggressive childhood cancer of immature nerves. The group has 7 PhD students developing research projects around neuroblastoma biology. One postgraduate student successfully defended her work and was awarded a PhD last month.

We are a dynamic group proud to be engaged in research, science communication and patient involvement. We do that through different initiatives. Throughout September, we will share many of them and invite you to keep following us on social media.

Our projects address topics related to neuroblastoma microenvironment, cell interactions, tumour resistance and the development of new therapies. To do that, we use 3D in vitro models, identify immunotherapeutic targets and evaluate extracellular vesicles.

We are always happy to answer questions and interact with the public. Follow us on our social media channels and read our blog to learn more about us and our research.

We are running a fundraising event, “A knit-a-thon,” on the 19^th of September. Stay tuned!

Thanks for reading, and we go ahead with neuroblastoma research!

Navigating Time and Tasks in the PhD Journey – The Struggles of Autonomy

Embarking on a PhD is an exhilarating endeavour. It offers the freedom to structure one’s own time. But this autonomy can be a double-edged sword; while providing a sense of flexibility and leisure, it also presents challenges in managing time effectively, prioritising tasks, and maintaining a productive schedule. In the context of a PhD, self-discipline and efficient planning quickly become the guiding stars of success.

The absence of rigid working hours requires a strong sense of self-motivation and discipline to stay on track. Without proper time management, it’s easy to fall into the trap of leisurely indulgence, neglecting the essential tasks and milestones that shape the PhD journey. Never before did I appreciate nagging parents, teachers or just people to which you could outsource motivation and feedback as easily. In a PhD, you’re on your own. You’re the only one who truly cares that what you’re working on is getting done. Done well and done at the right time. There is your supervisor, of course, and maybe collaborators. But it is not their job to stand behind you and say have you done this yet or that yet. They don’t see how much work you do or don’t do in a day. No one tells you to get off your arse when you’ve just stared at a blank screen for 20 minutes, and no one tells you to give it a rest when a simple problem turns out to be far more time-consuming and exhausting than expected because things still need to be kept moving. In the end, you can only rely on yourself to tell you whether you have worked enough or not. No one else knows. That can be extremely motivating and similarly defeating when you feel like you’ve done nothing but work for a couple of weeks and the results still aren’t there, so it seems like it doesn’t make a difference.

To conquer the time management challenge, prioritisation becomes paramount. As a PhD student, the spectrum of tasks can quickly seem overwhelming. Between different avenues and tasks that would progress your project, keeping up with writing, creating figures for adjacent projects, producing posters and presentations for conferences, writing blog posts, and making videos for funders and meetings, there always are more things to do in a day than could possibly be crammed in on the most productive of days. Figuring out how to manage urgency and importance becomes crucial to staying afloat. Identifying the most critical tasks and allocating time accordingly ensures progress and prevents the accumulation of unfinished work.

Maintaining a reasonable schedule becomes a balancing act. Especially when you pepper a couple of meetings in the very early morning because your collaborators are in a different time zone. And yet creating and adhering to a schedule is the foundation of effective time management. Despite the constant changes and different requirements, I find it helps immensely to establish a routine to cultivate discipline and maintains an easy overview over the week to allow myself to check what has been achieved and how long it took, so I can gauge how much more I need to do or whether I get to relax and leave half an hour early another day. It is crucial to strike a balance between focused research, data analysis, writing, and personal well-being. Regularly reassessing and readjusting the schedule as priorities shift guarantees that all aspects of the PhD journey receive the attention they deserve.

Navigating the realm of a PhD requires a delicate dance between self-motivation and effective time management. While the allure of autonomy can be tempting, the importance of prioritising tasks and maintaining a schedule cannot be understated. By striking a balance between work and personal well-being, the PhD journey can be transformed into a harmonious symphony of progress and achievement. Well, that’s the idea anyway.

As you embark on your own PhD adventure, you realise every day that time is a precious resource, and effective management is the compass that guides you toward success.

Written by Ronja Struck

Hello everyone! I’m Federica!

Hello everyone! I’m Federica, the new PhD student who joined the group 😃

I’m amazed that it’s been almost a month since it happened, and I couldn’t be happier!

I was born and raised in Palermo, a beautiful city in Sicily (Italy), but I always felt that it was not my place. So, I tried to combine my passion for cancer biology and my desire to live abroad by exploring the Erasmus Mobility Programme. I was awarded this scholarship twice, but both times I couldn’t avail of this opportunity. In March 2022, I got my Master’s degree and said to myself, “It’s time; this is my chance to go and build the future that I want”. And here I am. 😄

I moved to Dublin in June 2022 and loved this city’s vibes! I met wonderful people from all over the world with which I spent really fun and carefree moments.

These are only a few of that magic moments:

– I saw a deer for the first time in my life – I was soooo happy!

– I tried the “mate”, a traditional South American caffeine-rich infused herbal drink. As you can guess, I didn’t like it 😂 (sorry, my Argentinian friends).

– I got used to the outstanding colours of Ireland.

Obviously, I also had hard days. My English is still not perfect, but it’s getting better every day! I remember the first day I arrived in Dublin when I was looking for a cup, but I asked for a cupboard in three different supermarkets 😂. People looked at me, probably thinking: “Why is she looking for furniture in a grocery store? Should I say something to her?” I realized that I had asked for the wrong thing only during the night, when I was in bed, thinking about that first crazy day.

To be honest, I had a lot of really hard days, days when I felt that I wouldn’t be able to deal with other problems. But I never thought of giving up and returning to Italy. Every difficulty, every good or bad thing, is part of this wonderful experience, and I’m so excited and proud of myself for all the improvement I’ve been making, step by step.

I couldn’t make a better choice because I found my place in this super nice and great team in the Bioengineering Group 🙃

I look forward to better knowing all my new teammates and sharing with them my journey as PhD student!

Written by Federica Cottone

So this is science..?

Had you told me before I started my PhD that I’d rushedly be writing a blog post on a bus in Bergamo, and it’s all part of my project, I certainly would have laughed and figured sure, maybe as a one-time exception if I find out something fascinating. But no, this is my second conference abroad this year, out of five in the past 4 months. My view on science and what is important to conduct good science has significantly changed since then, though. I have a ton of data from my secondment to Vilnius, but it is not all analysed yet. There are a number of decisions left to be made before my project becomes fully rounded and provides useful conclusions that I could share with people. But conferences serve another purpose. If everyone was only there to present their finished project, who would they present them to? At the current stage of my research, exchanging ideas, receiving feedback and seeing what others do helps immensely to provide perspective and both motivate me to do more and do better, inspire me to find new angles and also to relax and understand the bigger picture your project is a part, rather than getting bogged down by the day-to-day issues that so easily cloud your mind in everyday routine (as far as a PhD allows for routine…). In this way, conferences can shape a project, inform analyses and provide far more than an excuse to be out of the office.

Even more enjoyable are, of course, conferences when they’re held in such beautiful places! I’d never been to Barcelona or Milan. While I have no intention of making the cultural metropolises of Athlone and Limerick pale in comparison, it does feel different when adding an afternoon of sightseeing, includes a couple of centuries-old towns that look like they fell out of a fairy tale and churches built in the 13 hundreds in 20 degrees in March rather than freezing your fingers off after just an hour outside or seeing some trees and an old pub. I never thought science would facilitate me seeing the world, but I am delighted that it does. And while I never would have expected it before, I can now appreciate the value of presenting your project halfway to ensure that it’s the best it could have been when it’s done.

Presented my project at the European Association of Cancer Research Conference on National Pathology because I was awarded the Organisation of European Cancer Institutes (OECI) travel grant. So, I could enjoy some of the stunning views in Bergamo and even visit Milan.

Written by Ronja Struck

Ronja’s Travel to Vilnius University and the National Pathology Centre

Ronja received a 3 months EACR Travel Fellowship to travel and learn new skills from RCSI Ireland to Vilnius University and the National Pathology Centre, Lithuania, between July and October 2022.

She reflected on her personal and professional experience in the EACR Cancer Researcher blog. Enjoy the reading!

Ronja PhD is supported by the Irish Research Council and the Conor Foley Neuroblastoma Cancer Research Foundation.