Profile

I live in Edinburgh with my husband and two children. I like to read crime and steampunk books and watch boxsets on Netflix. I love listening to podcasts and knitting in my free time. My favourite pizza is usually which ever one I happen to be eating and I have an unhealthy obsession with RuPauls’ Drag Race.

Sharing Things podcast episode

]I help organise the collection of tumour tissue samples and blood samples from patients enrolled in breast cancer clinical trials. These tumour samples are logged in our lab and then we process the samples to make derivatives such as:

• glass slides with unstained sections (thin slices of tissue 0.5mm thick)
• tissue micro arrays (tissue grids containing 198 cores from different patients)
• Extracted DNA
• Extracted RNA

These samples are then shipped to collaborators worldwide for analysis. We regularly ship to Toronto where our sister lab is and to America, Germany and soon to Australia.

https://blogs.ed.ac.uk/technicians/2020/12/16/whos-who-tammy-piper/[/embed

Check out the gallery on what the tissue bank and samples we look at look like!

After checking in with my lab colleagues on anything that may need my attention, I usually spend some time going through emails, working out budgets for the next project and reviewing different project protocols. I attend various trial management group meetings to either help plan out the tissue collection method for that particular trial or to give an update on what samples have come in and been processed. Things to consider when collecting tissue from clinical trial patients is to make sure they have given fully informed consent – this means they have been provided with information with what we need from them, how often they need to give a sample, what we plan to do with it and what happens should they change their mind. We also work with the research nurses at different sites to make sure they have everything they need for collecting the samples and to arrange couriers to collect them. I try to get all the trial reports updated in the morning so I can spend the afternoon working on image analysis.

When we analyse material from a trial, rather than produce one glass side per patient to then stain for the protein or ‘biomarker’ of interest and then review using a microscope, we produce tissue-microarrays. We basically take a small core (0.6mm in diamter) from each patient’s tumour tissue and place into a new wax block. Each block can hold up to 198 tumour cores so instead of looking at one slide per patient, we look at one slide per 18 patients. This saves us both time and costs and my eyesight! When I first started in the group we looked at all our biomarkers by eye which for one trial of over 4500 patients meant we looked at 4500 slides per biomarker, and we usually start with 4 different biomarkers. So for one project IO could have looked at over 16000 slides! By making tissue microarrays instead I looked at only 78 slides per marker.

Back in 2006, we analysed all the biomarkers by eye using a microscope and either estimating the percentage of tumour that stains positive or by actually click-counting the number of positive and negative tumour cells. Part of my role has been to test out different software that can do that counting for us and train it up to a standardized level where we can confidently use it for all our clinical trail analysis. I usually spend my afternoons either performing the quality assurance checks on what has been analysed or training up the software for the next biomarker.

Biomarkers we look at include oestrogen receptor, progesterone receptor and Her2, all growth hormone receptors that can encourage tumour cell growth . These are used routinely by pathologists to help indicate which treatment a breast tumour should respond to when diagnosing a patient. We use these biomarkers in research to see if we can be more specific in identifying which tumours will and which won’t or which will become resistant to that treatment. We also look at a biomarker called Ki67 which helps us see which tumour cells are proliferating or multiplying. We can take a tumour sample during a patient’s treatment schedule and compare the Ki67 level with the original diagnostic tissue to see of the treatment is having an effect on tumour growth.

Check out the gallery IMAGE ANALYSIS

for pictures of a TMA and the different biomarkers.