Tag: #neuroblastoma

#JournalClub: Anti-Cancer Immunotherapy

Hi there, Federica here! In the fast-paced world of scientific research, staying informed about the latest studies and breakthroughs is crucial. It enables researchers to build upon existing knowledge, avoid redundant efforts, and discover new directions for their work. That’s why we’ve started a new series of blog posts highlighting recent papers and explaining their significance for our research.

Recently, a fascinating study explored an innovative method to boost the effectiveness of cancer immunotherapy: “A combination of a TLR7/8 agonist and an epigenetic inhibitor suppresses triple-negative breast cancer through triggering anti-tumour immune“.

The researchers investigated a combination of immune checkpoint blockade (ICB) and other drugs to turn “immune-cold” tumours (which evade the immune system) into “immune-hot” tumours (which the immune system can attack). They developed a special delivery system using nanoparticles called metal-organic frameworks (MOFs). These nanoparticles were loaded with two types of drugs—a TLR7/8 agonist and an epigenetic inhibitor (BRD4 inhibitor). To make the nanoparticles even more effective, they were coated with vesicles from the cancer cells themselves. This coating helps the nanoparticles specifically target cancer cells.

But how does it work?

The nanoparticles are designed to find and enter triple-negative breast cancer (TNBC) cells. Once inside, the drugs prompt the cancer cells to break apart and release signals that alert the immune system. These signals attract dendritic cells, which then activate CD8+ T cells—the body’s natural cancer fighters. The TLR7/8 agonist further enhances this immune response, making the treatment more powerful.

In both laboratory tests and animal models, this method showed significant promise. It not only slowed down tumour growth but also improved the body’s immune response to cancer. Importantly, the study found that this approach could remodel the tumour environment, making it more hostile to cancer cells. For example, they wanted to verify that their combined delivery system could really boost the body’s ability to fight tumours. They focused on a protein called calreticulin (CRT) that, when it shows up on the surface of tumour cells, helps the immune system spot and remove them. They found that when they used their special delivery system (CM@UN and MCM@UN), the levels of CRT on the surface of tumour cells went way up. This was especially true for the MCM@UN group, showing just how powerful their method was in getting the immune system to attack the tumours.

The original image was published in J Nanobiotechnology. 2024; 22: 296.

So, why is this study important for my work?

The principles of enhancing the immune system’s ability to fight cancer are central to both the research in the study and in my project. Like the nanoparticles in the study, mRNA vaccines can be designed to specifically target cancer cells, ensuring that the treatment reaches its intended destination. Another similarity is how the drugs activate the immune system, which parallels how mRNA vaccines work—by training the immune system to recognise and attack cancer cells.

I find this study really interesting as it sheds light on innovative strategies for cancer treatment and provides valuable insights that can inform and inspire our research on developing mRNA vaccines for childhood neuroblastoma!

Written by Federica Cottone

Class 2024: Congratulations to Ciara, Ellen and Rabia!

Massive congratulations on the official moulding of PhD and MSc by Research to our promising young scientists: Rabia Saleem, Dr Ciara Gallagher and Dr Ellen King! Great accomplishments!

Three different journeys, with two through the COVID-19 pandemic. The full range of ups and downs. Who said that the PhD is a straight line? It has never been. It is more like the Irish weather: some days are sunny and bright, and some have scattered showers, gale winds and stormy snow, with sunshine developing elsewhere. The journey was spiced up with publications, conferences, travels, days out and fundraising events with the team.

It is a proud moment for me as well. 🙂 Three PhD and one MSc by Research students graduated within the last 12 months.

Of note, Ellen was behind our Twitter activities in the past, making our team visible!

Wish you all the best of luck on your new adventure!

Olga Piskareva

Congratulations to a new Dr in the house: Dr Ellen King

Huge congrats to a newly minted Dr Ellen King!  She passed her PhD viva on April 9. This is a testimony to your dedication, strong will and hard work. May this PhD be the beginning of many more successful endeavours, Ellen!

We thank examiners Prof Sally-Ann Cryan (RCSI) and Prof Joanne Lysaght (TCD) for the time and expertise they provided.

We also thank the RCSI PhD Programme for their generous support!

From left to right: Prof Joanne Lysaght, Dr Ellen King, Dr Olga Piskareva & Prof Sally-Ann Cryan

How things work in science: targeting cell components.

How do researchers study cells? How do we get the nitty gritty?

We use many methods to tag and chase various cell components. One of my favourites is fluorescent microscopy. It allows the use of nearly all spectrum of colours from blue to purple in one go. However, we prefer to narrow it down to 2-3 colours and avoid their overlap.

How does it work? First, we use DAPI or Hoescht, which are blue fluorescent dyes used to stain DNA. This way, we tag the nucleus of the cell. Then, we tag a protein of interest. In our case, it was MYCN, a protein that acts as a transcription factor. MYCN amplification is associated with poor prognosis in neuroblastoma. As a transcription factor, it binds to genomic DNA and is located in the nucleus. We used a specific antibody that was labelled with a green fluorescent dye. Look at the image below. The green colour pattern overlaps with the blue colour. Then, we tagged the cytoskeleton, a complex of various proteins that hold the cell architecture and dynamics. We used phalloidin with red fluorescence. It is a highly selective bicyclic peptide and a popular choice for staining actin filaments.

Neuroblastoma organoids stained with DAPI, Phalloidin and anti-MYCN antibody. This work was done during the Fulbright journey to Ewald’s Lab at Johns Hopkins

Now, we can enjoy visualising cells and test different research questions. For example, how do cells respond to a drug? Or how do neuroblastoma cells spread?

Written by Olga Piskareva

How things work in Science: Tìr na nÒg

In humans, NANOG, SOX2, and OCT4 are transcription factors that maintain the undifferentiated state of embryonic stem cells (ESCs). NANOG was first discovered in 2003 by Chambers et al. and Mitsui et al. as a transcription factor in ESCs responsible for cellular self-renewal. More importantly, it enables continuous self-renewal of cancer stem cells, leading to metastasis when the regulatory genes involved do not function normally. These have been identified as cancer stem cells, with NANOG being a marker of “stemness”. In multiple cancer types, NANOG has various effects, including cellular expression of mesenchymal phenotype, cellular invasion/migration, repressed apoptosis, drug resistance, and increased angiogenesis. In pathways, NANOG either promotes or represses the expression of other genes that lead to cancer-favoured cellular behaviour. Overall, a higher expression level of NANOG is usually indicated in cases of poor prognosis.

NANOG is even more interesting due to its eponym, which comes from Tìr na nÒg. A Celtic myth of the Land of Youth, where the Tuath Dé resided in a supernatural land of paradise. This land offered beauty, health, joy, and everlasting youth to the inhabitants. As the myth goes, the Tuath Dé were gods of the land, and the god that ruled, Manannán mac Lir, was the first ancestor of humans. In various Celtic legends, humans are invited by the gods to visit Tìr na nÒg on great adventures.

However, time passes much slower in Tìr na nÒg, making it precarious for humans to return to their own world. As is the fateful tale of Oisín, who fell in love with the Tìr na nÒg goddess, Niamh. He travelled with her to Tìr na nÒg, where they lived happily in paradise. Upon a visit back to Ireland, Oisín realized that all his family had died over the years. When Oisín found a group of men who were struggling to move a giant rock, he stopped to lend them a hand while on his horse. However, the weight of the rock caused his saddle strap to snap. He fell from his horse, and when he touched the ground, he suddenly aged 300 years all at once.

Written by Alysia Scott

Sources:

Gawlik-Rzemieniewska, Natalia, and Ilona Bednarek. “The role of NANOG transcriptional factor in the development of malignant phenotype of cancer cells.” Cancer biology & therapy vol. 17,1 (2016): 1-10.

“The Story of Tír Na NÓg.” Celtic Titles, 10 Feb. 2022

Congratulations to Dr Ciara Gallagher!


Huge congrats to a newly minted Dr Ciara Gallagher!  She defended her PhD on March 8 – International Women’s Day. Your enthusiasm and perseverance are truly fascinating! May this be the stepping stone towards a brighter future, Ciara!

We thank examiners Dr Marie McIlroy (RCSI) and Prof Jan Škoda (Masaryk Uni) for the time and expertise they provided.

We also thank the Irish Research Council for their generous support!

Dr Ciara Murphy (Chair), Dr Olga Piskareva (Supervisor), Dr Ciara Gallagher, Prof Jan Skoda (examiner), Dr Marie McIlroy (Examiner)

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

International Childhood Cancer Day – 15 February 2024

We are celebrating #ICCD2024 with a Bake Sale and a Quiz. To earn a piece of cake, you have to answer a question correctly! Have a look at some:

  • Which civilisation first described cancer?
  • Where did the word cancer come from?
  • Do children get cancer?
  • What is the most common type of cancer in children?
  • Can the Human Papillomavirus (HPV) vaccine prevent cancer?
  • Can neuroblastoma begin to develop before birth?
  • What is the name of the nerve cell in which neuroblastoma begins to grow?
  • Can a child have a genetic predisposition to neuroblastoma?
  • What % stands for the incidence of neuroblastoma: 8 or 15?
  • What % stands for the neuroblastoma-related deaths: 8 or 15?
  • Does neuroblastoma first appear in the brain?
  • What does the letter N stand for in the gene MYCN?
  • How often does childhood cancer occur compared to adults?
  • How often does hereditary cancer happen in general?
  • Do you think that children are small adults when we talk about anticancer treatment?

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

Congratulations to Dr Cat Murphy!

November 22, 2023 – Catherine was officially coined Dr Catherine Murphy. A Big Day for Catherine, her family and me.

Catherine joined our team in July 2019 to carry out a research project funded by Neuroblastoma UK. In this project, she aimed to use 3D culturing to engineer a novel experimental model and study the biology and immunology of neuroblastoma, an aggressive childhood cancer. There was the full spectrum of challenges and hard work spiced up with the uncertainty of the COVID-19 restrictions!

The PhD journey is never a straight line. It has a range of colours with 50+ shades for each. There are black alleys and hidden cul de sacs. Between July 2019 and June 2023, some days were sunny and bright, and some had scattered showers, gale winds and stormy snow, with sunshine developing elsewhere. The journey was spiced up with publications, conferences, travels, days out and fundraising events with the team.

Of note, she was behind our Twitter activities and blogging #AskCat, making our team visible! All these together have moulded into a new multi-skilled professional – Dr Catherine Murphy!

Well done to Catherine! Wish you the best of luck in your new adventure!