Developing new methods for studying human heart biopsies 

To better understand the background of Jonathan’s article regarding heart disease, researchers need access to human heart tissue which is naturally scarce - while animal models provide important insights, according to Jonathan: “Animal models cannot fully capture the unique complexity of the human heart or the wide variability seen in patients. So, to truly understand human disease, we eventually need to study actual human heart tissue, but these samples are rarely available for cardiac research”. 

At the same time, hospitals have been collecting and storing human heart biopsies for decades as part of routine care. These tissues are preserved as FFPE (formalin-fixed, paraffin-embedded) blocks and “hold enormously valuable clues about how diseases manifest, but the chemicals used to preserve them make the proteins incredibly difficult to extract and analyse”, Jonathan explains. Thus, Jonathan embarked on a journey to change that through his project. 

Utilising archived tissues to learn more about earlier disease and rare conditions

Over the past years, Jonathan and his colleagues have developed a method that turns these archived tissues, some decades old, into a reliable source for deep proteomic profiling. Jonathan’s work focuses on proteomics - the study of proteins, which are the "workhorses" of the body that carry out nearly all biological functions. By studying these proteins directly, he can see how the heart's molecular machinery is functioning. This approach allows Jonathan and his colleagues to measure thousands of proteins at once and relate the molecular insights to patients’ medical histories, helping to reveal proteins that may be linked to heart disease.

Jonathan was motivated by the idea that such valuable specimens are largely sitting unused in hospital archives. Hence, accessing them could be the key to learning more about earlier disease stages and rare conditions while taking advantage of the rich clinical metadata linked to each sample. Jonathan also calls this: “an exciting technical challenge”, as he is combining method development with biological discovery and strong translational potential.

Challenges when working with real human samples

When reflecting on the first steps of this project, Jonathan explains that the primary hurdle was technical: “the preservation process creates chemical changes that make proteins inaccessible,” he says and adds: “we had to carefully refine our methods to overcome these barriers and ensure we could get consistent, reliable results from every sample.” 

Beyond the chemistry, the physical nature of the tissue added another layer of difficulty. Clinical biopsies are often tiny, sometimes smaller than a grain of rice, which means they must be handled with extreme care and analysed with highly sensitive methods. “There is no room for error when working with such limited and precious material,” Jonathan emphasises.

Once the method was validated, it was time to put it to test. Jonathan’s team turned to two areas of high clinical interest; the sinus node and biopsies from patients with ACM. According to Jonathan, working with real human samples is always a balancing act, as “variables can’t be controlled retrospectively, and finding perfectly matched cases and controls can be challenging”. 

Finally, after generating the data, the team had to analyse and interpret the vast layers of biological information. During this period “keeping up with rapidly evolving instrumentation and methods” was another challenge for Jonathan and his colleagues which required continuous adaptation.

Providing more personalised approaches to patient care

Throughout the project, Jonathan has worked closely with colleagues from both technical and clinical backgrounds, not only to develop and refine the methods but also connect the work to real patient samples and cases. These collaborations across different perspectives were “a really valuable learning experience”, Jonathan says, giving him a clear sense of what translational research is. 

With this project, Jonathan hopes to make proteomics more accessible to cardiac researchers who already have, or could have access to, archived FFPE tissue, increasing the value of these samples and shifting the focus toward directly studying clinical material. According to Jonathan, this approach enables protein characterisation at scale, which could reveal potential biomarkers and therapeutic targets.

The datasets generated through this project, including detailed molecular maps of specialised heart regions and disease-associated changes, illustrate the lasting potential of proteomics to deepen our understanding of the human heart. According to Jonathan: “these findings help advance cardiovascular research and could ultimately inform more personalised approaches to patient care”. 

Improving cardiovascular research in the future

Looking ahead, Jonathan hopes to make better use of the rich resources that are already available and improve patient outcomes by enabling more in-depth study of material that has already been used for histopathological evaluation but could yield even more information. Over time, he also hopes proteomics will play a greater role in molecular phenotyping, contributing to a broader vision of molecular diagnostics that goes beyond genetics alone.

The next steps for Jonathan’s research are to further refine his methods to make the most of limited material. This could be done, according to Jonathan, by achieving “cell type–specific readouts or mapping tissue microarchitecture”. In addition, Jonathan aims to use archived samples to uncover disease signatures across larger patient cohorts and evaluate how well proteomics can classify biopsies by cardiac disease state. Ultimately, Jonathan’s goal for the future is to improve our understanding of how the heart works, reveal the molecular changes behind disease, and support better approaches to diagnosis and treatment by taking advantage of already available resources of human heart tissue. 

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3 key findings in Jonathan’s project

In Jonathan’s recent publication, he highlights 3 main findings: 1) A “recipe” for proteomics of FFPE heart tissue, 2) New biological insights into the pacemaker of the heart, and 3) hallmarks of arrhythmogenic cardiomyopathy (ACM). 

The first finding, a standardised protocol (“recipe”) for proteomics of FFPE heart tissue, showed that decades of archived human tissue could now be used for molecular studies of clinical specimens. Jonathan highlights how his group benchmarked a workflow that yielded high-quality data comparable to fresh tissue (the current gold standard), enabling retrospective studies on large collections of human samples.

A second noteworthy finding was new biological insights into the pacemaker of the heart. They profiled the human sinus node, a tiny, specialised structure that sets and regulates the heart rate but is notoriously difficult to isolate. They identified hundreds of proteins that are especially abundant in the sinus node, highlighting pathways such as GPCR (G Protein-Coupled Receptor) signalling an extracellular matrix organisation that likely underlie its pacemaking function.

Finally, through their ACM case study, the team applied this method to a disease in which structural changes in the heart are well characterised but can be patchy and difficult to capture in small biopsy samples. They found that FFPE-based proteomics could clearly distinguish hearts from ACM patients versus healthy controls, demonstrating the diagnostic potential of the approach. Beyond this, the data revealed specific proteins and pathways uniquely altered in ACM, offering new insights into the molecular mechanisms underlying the disease. This finding illustrates how proteomics could add a deeper layer to traditional pathology. 

Overall, the findings showcase how researchers can use archived tissues of the human heart to learn more about cardiovascular diseases on the molecular level which could ultimately guide future interventions.