The Promise of Precision Pathology

Precision healthcare is the future – of that, I have no doubt. But how do we go about successfully developing it for the patients who need it? The key, in my opinion, lies in the comprehensive availability of high-quality human samples for all aspects of research – from basic bench work to clinical trials. And who better to ensure that availability than pathologists? Pathology is the central specialty of personalized precision medicine. It is pathology that provides the skills, infrastructure, and scientific vision we need to lead the way in science-driven biobanking, and it is pathology that can help to ensure optimal research use of human samples. And that’s why my pathology colleagues and I have taken on the task of setting up a major new initiative at Memorial Sloan Kettering Cancer Center – the Precision Pathology Biobanking Center (PPBC).

Founded in 2015, the PPBC represents an institution-spanning collaborative research center that is being built around five highly interconnected pillars (see Figure 1): next generation, “future-proof” biobanking; “big data” computer science and database development; a hub for developing and evaluating the next wave of theranostic pathology technologies (like proteomics, metabolomics, and molecular imaging); a hub for pathology to take on a proactive role in the latest generation of specimen-driven clinical trials and drug development; and a platform for pathology to develop strong joint research, development and commercialization partnerships with the private sector. It’s easy to see how a thoroughly annotated, high-quality biobank underpins every one of these pillars.

Building a better biobank

When we designed the PPBC’s specimen acquisition, preservation, storage, and distribution workflows, the concept of “future-proofing” was front and center: all samples (tissues, bloods, other liquids) are procured at high speed (ideally directly in the operating rooms or interventional radiology suites) and uniformly held in vapor-phase liquid nitrogen, rather than dry ice or -80°C freezers. Previous research has convincingly shown that some of the most interesting components of the pathophysiome – like RNA, post-translational modifications of proteins, or small metabolites – degrade unpredictably, even at -80°C, over time spans of months to a few years. In vapor-phase liquid nitrogen (which cools to below -160°C), on the other hand, they remain stable – thermodynamics is one’s friend. The PPBC banks specimens from approximately 7,000 new cancer patients per year, including surgical resections, interventional radiology biopsies, and companion blood and body fluid collections – so we certainly don’t want to lose those samples just a few years down the road.

How do we prepare our samples? Lesional and matched normal tissues are flash-frozen in liquid nitrogen without further additives; then, we prepare spatially indexed formalin-fixed and paraffin-embedded (FFPE) blocks that match each sampling location of a corresponding frozen vial. Blood (frequently both pre- and post-treatment) is processed into frozen serum, plasma (double-centrifuged for use as a source of circulating free DNA), and buffy coat (white blood cell) aliquots. Of the more than 30,000 specimen units we create annually, over 1,600 units of frozen samples and 1,000 units of FFPE material are used for immediate research. The rest of the material isn’t simply relegated to long-term storage, because we have many innovative projects underway. For instance, a significant and rapidly growing portion of the PPBC’s activities (amounting to about 1,700 units of fresh samples) is related to “living” biobanking – the creation of organoid cultures (see Figure 2), mouse xenografts, primary cell lines, and so on.

Our biobank division has developed innovative QA/QI metrics and processes, including RNA integrity monitoring in sentinel samples and participation in international proficiency testing schemes, such as the International Society for Biological and Environmental Repositories’ Integrated Biobank of Luxembourg program (see “Curating Pathology’s Future”). Most importantly, we made a strategic decision early on to embed our research biobanking activities intimately into existing clinical workflows. One good example is our rapid tissue acquisition setup, which takes samples from the point of acquisition to liquid nitrogen storage in less than 15 minutes. We accomplish that by pairing up licensed pathology assistants (PAs) with biobank technicians according to daily schedules and making sure that the clinical PAs assigned to biobank service on any given day aren’t distracted by clinical responsibilities on those days, letting them dedicate their time and effort fully to research biobanking.

Informatics impact

A physical repository of biospecimens is only as good as the level of annotation and knowledge that can be associated with each and every specimen in the bank. Recognizing that data federation (the aggregation of disparate data sources), research databases, and smart “big data” query tools remain a major challenge, the PPBC has started to put significant effort into developing innovative data informatics and computer science tools (see Figure 3). We feel strongly that pathology as a discipline will increasingly evolve into the medical specialty of dynamic data management and big data integration to drive patient care – theranostics – rather than the status quo of “just” providing a static diagnosis.

Translated to biobanking, it means we need to build tools that cross-reference physical samples in real time to all other data we may have on a patient (clinical status, therapeutic status, imaging results, clinical trial participation, molecular features of the disease, and any other relevant information). We attempt to build a longitudinal representation of every patient, from diagnosis through stages of treatment and recurrence to long-term follow-up. We map each physical sample onto a common timeline along with all other observational or interventional medical events. For example, we could ask, “How many frozen research samples containing cancerous tissue does the bank hold from patients born after 1960 with a diagnosis of KRAS-mutated colon cancer (see Figure 4)?” As convoluted as that sounds, we can readily build much more complex Boolean queries on the fly and still have results within seconds. And it’s not just to show off the power of our data organization. Queries like that one have already become instrumental tools for feasibility arguments in grant submissions and hypothesis generation for numerous biomarker studies – and we foresee even greater possibilities for them in the future.

Technology marches on

A pathology-controlled biobank is a major scientific asset for our discipline. We are currently at the beginning of a wave of disruptive technologies that I predict will become essential in our diagnostic and theranostic toolsets. With next generation sequencing reaching technological maturity in clinical laboratories, we already see new technologies (such as mass spectrometry-based deep proteomics, functional assessment of pathway activities, metabolomics, highly multiplexed immunofluorescence, ex vivo living models of drug response, and more) that promise to change the way we will assess and monitor disease.

By tightly integrating biobanking into the PPBC’s overall mission, the real-life evaluation and clinical assessment of new technologies becomes a natural fit. At the moment, we are assessing high-resolution Orbitrap liquid chromatography-mass spectrometry (LC-MS) as a highly quantitative, highly multiplexed tool that can precisely measure several thousand proteins in tissue in parallel. If it works the way we hope, it will be able to complement – if not replace – conventional immunohistochemistry. And not only does mass spectrometry require no antibodies, but it can also directly detect mutations at protein level and post-translational activation states, such as phosphorylation. So why are we the perfect testing ground for such innovations? Most new technologies require living and biobanked samples of the highest quality. Conventional FFPE-based clinical archives are either suboptimal or altogether unusable for these applications. Cutting-edge, forward-looking and science-driven biobanking is clearly the way forward.

Trying out trials

Pathology has not historically been a driver discipline in clinical trials or drug development, with its role often limited to providing slide review for patient enrollment or sending FFPE material to third-party trial sponsors. In the era of what I like to call “specimen-centered, molecularly driven” clinical trials (for instance, basket trials like NCI-MATCH), pathology’s role is rapidly changing and our discipline is becoming a central player. This development has significant ramifications for pathology training and education, as well as for our understanding of pathology as an increasingly clinical discipline.

The PPBC has a division that provides a dedicated platform for pathology’s representation at every stage of a new clinical trial; it includes design, protocol writing, budgeting, direct discussions with sponsoring pharmaceutical companies, specimen acquisition, companion diagnostic development, and any other aspect you can imagine. To provide just one example, we’ve created a dedicated Phase I biobank for patients on first-in-man clinical trials that provides an unmatched resource for research. We believe pathology belongs at the forefront of new medical science, and we’re pulling out all the stops to make sure it gets there.

PPBC R&D partnerships

The combination of comprehensive biobanking and new technologies provides a natural, externally visible infrastructure that now allows the PPBC – and pathology as a discipline – to engage directly with the biotechnology and pharma sector. We are enabling pathologists and commercial entities to carry out joint projects, such as co-development of new companion diagnostics, evaluation of biomarkers, or the use of new instrumentation. Such projects frequently hold opportunities for intellectual property generation. And there are even more tangible benefits; research biobanking is often difficult to support through traditional funding mechanisms, so funding raised through research and commercialization can represent a major contribution to its long-term sustainability.

We’re at an exciting junction in pathology’s growth as a medical specialty, and I’d say it’s becoming clear that pathology-driven biobanking is both central to our core expertise and, even more importantly, a powerful enabler for many of the most promising growth areas of our discipline: precision healthcare, clinical trials and drug development, theranostics, and functional assessment and monitoring of disease. I’m eager to expand biobanking’s role in pathology, and eager to see where this new platform can take our discipline next.