Ever had a biopsy taken? Ever thought about what happened to it next? Dr Féaron Cassidy sat down with clinical pathologist Dr Victoria Malone to find out.

What happens after a biopsy is taken?

When a biopsy is taken, we might think about what the results may be, or try not to, but we rarely think about how that result is actually determined. The sample is sent off, and days later a result comes back. But between those two points lies one of the most important, and most hidden, parts of medicine: pathology.

I recently spoke with Dr Victoria Malone, a clinical histopathologist at St James’s Hospital in Dublin, to better understand what actually happens to a tissue sample, and how those results shape decisions about diagnosis and treatment.

So, where does my biopsy go?

Not to a black box, or a magic machine, but to a person called a “pathologist”.

Once a biopsy arrives in the pathology lab, the whole piece of tissue is carefully examined. This will be quick process for a small biopsy, but sometimes large tumours removed during surgery are brought to pathology, in which case, the initial assessment can take hours. Assessment of a tumour removed during surgery includes things like checking that the edges of the removed tumour are actually non-cancerous tissue, to confirm no sliver of tumour was left behind after surgery. Pathologists then submerge the whole biopsy into formalin to prevent it from breaking down, and then into specialist wax. The wax is hot, and therefore liquid, when the tissue is added, it is then solidified at room temperature with the tissue inside. The wax means the tissue will hold its shape while being cut with a thin razor blade and when the resulting thin sections are placed on microscope slides. The technique of preserving pieces of biological tissue in formalin and wax has been used by scientists and doctors for well over 100 years. We call it FFPE (formalin-fixed paraffin-embedded).

Now that thin slices of the tissue sample are attached to microscope slides, the pathologist will use a variety of dyes and stains to colour it before looking at it under the microscope. These stains can be for specific gene expression or protein, but by far-and-away the most commonly used staining is a combination of two dyes (Haematoxylin and Eosin), and it is called H&E staining. H&E staining turns different cells in the tissue different shades of pink and purple, allowing pathologists to identify them. Vicky explains to me that pretty much every single sample that comes to her in the pathology lab will be stained with H&E as a first port of call.

At this stage, they are asking some of the most critical questions in medicine. Often this process looks like:  “Is this cancer? If so, what type? Has it spread? Are there features that will affect treatment”.

How do doctors decide what to do next?

For many cases, that initial examination with H&E staining provides a clear answer. Either the patient can be informed that they are all-clear, or they can be given a diagnosis. Often pathologists can provide extra information to the doctor treating the patient – such as the type, stage, as well as any clues as to what treatment might work best for the patient. For example, pathologists can use specific stains to find out whether a breast cancer is likely to respond to hormone therapy, or whether a tumour may be suitable for immunotherapy. In some cases, molecular testing is also performed to look for specific genetic changes. These can be rare, but crucial for those patients who could benefit from targeted therapies. Because of the important role they play in classifying all aspects of tumour biology, pathologists are central to multidisciplinary team meetings, where clinicians from different specialities come together to decide on the best course of treatment, usually for cancer patients.

Sounds important right?!

Dr Malone described to me how one thing she loves about her job is that a single day’s work can influence decisions affecting dozens of patients, often across multiple specialties.  Despite this, pathology remains largely invisible to the public. Part of the reason is that, when it works (which is most of the time), it works quietly and effectively.

What about the challenges of working in pathology?

Biology is never straightforward so I know that any job dealing in trying to classify biological entities into distinct categories will encounter challenges ! As well as that, in my own research I have been working with a technique called spatial-omics. This is a technique that allows scientists to be able to assess hundreds or more different specific signals in a single tissue section at once. These are the same gene expression and protein signals that pathologists can currently assess, but currently pathologists can only assess up to a handful of these at a time, requiring a separate section of the tissue each time a new test is run. I believe that there is an important future for spatial-omics in clinical diagnostics (i.e. in pathology departments), as pathologists could use it to investigate numerous questions at once, rather than having to do tests one after another. However, before talking to Vicky, I already know there are hurdles to overcome before that could be a reality, and some reticence from the pathology community that it will ever take hold. Some hurdles will be easily overcome as the technology matures, such as ensuring standardisation for the technique. Other challenges are more complex and will take experts from different fields working together. For example, pathologists are concerned that a test which produces hundreds or thousands of results will lead to confusing, contradicting information which would be impossible to interpret. Scientists are looking to AI for solutions to ensuring understandable and useful data is generated from spatial-omics, but we are not there yet. I know that talking to someone who is working day-in day-out in a pathology suite will give me the insight to direct my research. Dr Malone’s lived experience could indicate whether spatial-omics in clinical diagnostics in a pipe-dream that pathology suites are better off without, or whether there are current challenges and needs experienced by those doing this important work that could be met by access to spatial-omics in the future. I am all ears to hear what Vicky has to say on this.

Dr Malone explains how valuable the tissue samples from patients are. Often a patient has had to experience an uncomfortable procedure for the biopsy to be taken. Biopsies are becoming smaller over time as procedures are modified to be safer and less uncomfortable for patients. At the same time, the expectations placed on each sample are growing. As we develop better medicines, and more personalised treatments to target the specific drivers of disease, more tests and more details are required from the samples sent to pathology. This creates a very real challenge: how to get the maximum information from a limited amount of tissue. I immediately note this as an important need that pathologists have that spatial-omics could meet in the future, and mention this thought to Vicky. She agrees, emphasising potential for particular value in cases where tissue is limited, or where many different tests are currently needed.

Vicky also talks about how one of the major challenges of pathology is that some samples don’t fit neatly into established categories, making it hard for pathologists to classify them. I am heartened to hear the collegial solution pathologists have come up to handle these uncommonly uninterpretable samples – they help each other out. Pathologists routinely seek second opinions on difficult cases. Results are interpreted alongside clinical information and imaging, ensuring that no single test result is considered in isolation. It’s also why understanding that all diagnostic tests have limits is so important. A result is a powerful piece of information, but it is one part of a bigger picture that includes symptoms, clinical judgement, and follow-up where needed.

Looking ahead, the future of diagnostics

After talking to Vicky I feel assured that there is a place for spatial-omics in pathology labs of the future, in combination with the tried-and-tested approaches of traditional microscopy, digital pathology, and molecular testing – an additional useful tool in the belt of pathologists. An important take-home regarding where spatial-omics needs to improve to be useful to pathologists is that the goal is not just more data, but better, clearer answers that can directly benefit patients.

That’s my take-home, what about yours?

I think it is that while pathology may be hidden from view, its impact is anything but. So next time you hear that a biopsy has been sent for analysis, it’s worth remembering what happens behind the scenes. That small piece of tissue is the focus of a detailed, highly skilled process that plays a central role in guiding diagnosis, treatment, and ultimately, patient care.