With the advancement of diagnostic technology and the pursuit of precision therapies, the use of microsatellite instability (MSI) and KRAS mutational profiling continues to grow in clinical practice. These tests identify genetic alterations in tumors, playing a crucial role in diagnosis, prognosis, and treatment guidance for several cancers.

To broaden our understanding of the role that MSI and KRAS gene mutations play in cancer, and potentiate new applications for these biomarkers, robust testing of diverse sample types from various cancers is needed. Discovery Life Sciences (Discovery), a leading biospecimens expert and specialty services provider, is playing a pivotal role in this endeavor. Discovery owns the world’s largest commercial biobank and procurement network and provides a diverse portfolio of multi-omics services. Discovery can test thousands of biospecimens simultaneously and is harnessing this sheer volume with unmatched technological prowess to help researchers better understand the underlying drivers of cancer.

CLN spoke to Dr. Shawn Fahl, Vice President of Lab Operations, Cell Services & R&D, Biospecimens at Discovery Life Sciences about the company’s work.

Can you discuss why you implemented fragment analysis-based MSI testing and Sanger sequencing-based testing for genetic biomarkers, such as KRAS, in formalin-fixed paraffin-embedded tissues (FFPE)?

We have a large repository, and we wanted a highly targeted analysis on clinically relevant biomarkers. Many technologies in our industry tend to provide extensive data. But in this case, we wanted something very specific and user-friendly. We also wanted to put together a well-defined, end-to-end workflow that simplifies the need for complex pipeline builds and provides seamless processing and analysis from specimen intake to data delivery.

Sanger sequencing isn’t exactly out of style, but it’s not the only method used anymore. Why did you decide to go this route?

There has been a significant shift towards next-gen sequencing, offering an excellent way for obtaining comprehensive genomics data. Discovery’s own Genomics Services lab right down the hall performs NGS studies for thousands of samples a day. That said, we’ve been noticing an increase of Sanger sequencing projects, largely because of its more targeted nature. The analysis is easier, and the footprint for running Sanger sequencing from start to finish is minimal.

A case in point: We have labs here in the U.S., where I’m located, as well as in Bulgaria, where a lot of Discovery’s clinical sites are located. Implementing Sanger sequencing in our Bulgarian labs allow us to be more efficient operationally.

What is the rationale behind retrospective annotation of a biorepository?

This is where much of our focus has been because we started as a biobank with a reliable biospecimen procurement network. We have millions and millions of specimens.

But having an extensive repository does not necessarily mean the specimens have annotations of the most current clinically relevant biomarkers. Leveraging our integrated multi-omics service capabilities, we are able to go back and test our inventory retrospectively, accelerating research and clinical projects.

What advantages does a characterized biorepository have over uncharacterized samples?

An enduring lesson from my time in graduate school resonates: We have solved cancer in mice hundreds of times, but we have not done it in humans. The intricate nature of human biology, marked by a higher level of complexity, makes cancer research significantly more challenging.

At Discovery, we aim to minimize data noise by meticulously controlling as many confounding factors as possible. That’s why pre-characterizing our biorepository gives us many advantages, and this proactive approach allows us to gain clearer insights and enhance the reliability of our findings.

In the biorepository, do you have a single sample type per patient, or do you have matched specimens across multiple sample types?

One of our priorities involves the strategic acquisition of new matched specimens from the same consented patients. We actively look for matched FFPE and fresh tissue samples, with the latter providing fresh viable cells, giving us the ability to conduct additional studies that may not be feasible with FFPE tissue samples. Moreover, we have started to collect tissue and blood from the same patients simultaneously.

The idea is that patients can undergo a blood draw, enabling us to monitor disease progression and evaluate the success of treatments based on circulating tumor cell-free DNA (ctDNA) at the same time.

In addition to FFPE, are there other biospecimen types you have tested for MSI or Sanger sequencing?

One we are most excited about is that we have started to run MSI and Sanger sequencing testing on tumor DNA circulating in blood. By analyzing ctDNA, we have successfully detected MSI high patients and KRAS mutations. This marks a transition from the traditional reliance on tissue testing to the promising potential of blood-based diagnostics or liquid biopsies.

Can you discuss any multi-omics evaluation you have performed using MSI/KRAS-characterized biospecimens?

Our unique advantage lies in our comprehensive approach to multi-omics. Extensive work has been dedicated to studying MSI and KRAS across different platforms. We’ve evaluated common immuno-oncology markers through flow cytometry.

Initially exploring PD-L1, PD-L2, and PD-1 proteins, we observed a lot of correlations with these markers. Then, we shifted our focus to more novel markers such as the inhibitory receptor TIGIT, along with CD226, CD112, and PVR proteins. These less-explored markers provide fresh perspectives compared to the extensively studied PD-L1/2. We have also moved into single cell transcriptomics, where--rather than limiting our scope to 20 genes or markers--we’re examining thousands. This approach allows us to discover new biomarkers, tapping into the vast landscape of human genomes.

Have you utilized MSI/KRAS-characterized biospecimens to develop new tumor models?

This is an area we are looking forward to. Leveraging our abundant collection of viable frozen tumor tissue, we have the ability to cultivate and test new compounds. Adapting human tumor specimens to grow in a cell culture dish is a challenging process. However, we've found success using long cell tumoroid models within a gel-like extracellular matrix.

The prospect of creating new drugs for specific KRAS mutations is generating considerable interest. We're exploring the possibility of generating tumor models from dissociated colorectal tumor cells to establish a comprehensive bank of targeted tumors. These models can then be swiftly tested in vitro against various drug compounds, given that we already have the parent materials. This approach allows us to quickly and precisely address targeted questions based on the characterized samples in our possession.

What do you hope for in the future with this technology?

I would love to see this technology utilized more broadly, especially with Sanger sequencing. Despite its decline in popularity with the rise of next-gen sequencing, Sanger sequencing has the advantage of speed, providing faster turnaround times when focusing on a defined set of targets with a more straightforward and consistent approach.

I think Sanger Sequencing holds the potential to play a more significant role in clinical settings. The ability to swiftly examine genes, particularly with the increasing prevalence of liquid biopsies, could make this technology exceptionally valuable in clinical applications.

Jen A. Miller is a freelance journalist who lives in Audubon, New Jersey. +Twitter: @byJenAMiller