Molecular Testing and the Future of Diagnosing Thyroid Cancer

Endocrine Society member and medical director for Endocrinology for Veracyte, Joshua Klopper, MD, talks to Endocrine News about a new tool that may have the potential to guide thyroid cancer management decisions by predicting tumor behavior via molecular signatures.

In “New Data Presented at the 2023 ATA Annual Meeting Demonstrate that Veracyte’s Afirma-Based Testing Can Uncover Key Molecular Hallmarks of Thyroid Cancer,” published online in Business Wire last September, Joshua Klopper, MD, medical director for Endocrinology for Veracyte, a genomic technology company specializing in cancer diagnostics, explains what novel molecular insights for thyroid nodules and cancer are enabled by preoperative analysis with the Afirma Genomic Resource for Intelligent Discovery (GRID), a research-use-only tool that is derived from the company’s Afirma Genomic Sequencing Classifier (GSC)

“The fundamental difference between the Afirma molecular testing platform and any other commercially available testing platform is the whole transcriptome–derived assay. As opposed to a panel of genes or a panel of microRNAs, almost everything that is expressed as mRNA is sequenced with Afirma GSC,” Klopper says. “We strongly believe that assessing mRNA and what is transcribed is the best indicator of what’s going on because a mutation that may be seen in DNA can sometimes be silenced. We’re sequencing everything that’s expressed out of those genes, so we’re sitting on a huge treasure trove of molecular data, not only with each nodule but with our entire database. We believe this resource can enable new discoveries to help advance care for patients with thyroid nodules and cancer.”

Veracyte’s data and analytics team can then cultivate novel signatures and report the different genes that are expressed by carving them out of the database. “So, GRID — it’s in the name — it’s a resource. Our expectation is that it will expand over time,” Klopper says.

Potential Treatment Stratification

Afirma GRID is modeled on the company’s Decipher GRID tool that has been used in prostate cancer research since 2015 and includes more than 400 gene signatures. Klopper says they hope to do for thyroid cancer research with Afirma GRID what Decipher GRID is doing for prostate cancer research. “We’re not quite there yet, but the posters we presented at the American Thyroid Association demonstrated different potential aspects of what can be provided by doing this whole transcriptome–derived analysis,” he adds.

“We strongly believe that assessing mRNA and what is transcribed is the best indicator of what’s going on because a mutation that may be seen in DNA can sometimes be silenced. We’re sequencing everything that’s expressed out of those genes, so we’re sitting on a huge treasure trove of molecular data, not only with each nodule but with our entire database.”

Joshua Klopper, MD, medical director for Endocrinology, Veracyte, Denver, Colorado

For example, with the “Sodium Iodide Symporter (NIS) Expression in Cytologically Indeterminate and Malignant Thyroid Nodules” poster, Prasana Santhanam, MBBS, MD, from the Johns Hopkins University School of Medicine and team analyzed over 47,000 thyroid nodules and demonstrate that NIS gene expression is differentially expressed based on the presence of molecular variants, such as high expression in thyroid nodules with a TSH receptor variant and lower expression in nodules with a BRAFV600E mutation. Additionally, they show that NIS expression declines as thyroid tumors become increasingly more oncocytic and neoplastic.

Because NIS activity is required for radioactive iodine uptake, these findings can potentially aid in the treatment and monitoring of differentiated thyroid carcinomas when radioiodine therapy is indicated. “We can report the NIS expression level and seek differences among the different kinds of nodules and different mutations,” Klopper says, which may ultimately lead to potential treatment stratification.

A Promising New Approach?

The “Leveraging RNA Sequencing for Pre-Operative Immunophenotyping of BRAFV600E+ Thyroid Nodules” poster from Jarod Olay, MS, from the UCLA David Geffen School of Medicine and team likewise offers a promising new approach to preoperative assessment of thyroid tumors.

The team performed a retrospective analysis of nearly 48,000 thyroid nodules. “We know that the immune system can promote or inhibit cancer responsiveness,” Klopper says. The findings suggest that the Afirma GRID immunophenotype gene expression may one day help predict thyroid cancer response to immune checkpoint inhibitor therapy using preoperative immunophenotyping rather than postoperative immunohistochemistry.

In the “Molecular Assessment of Isthmus Thyroid Carcinomas” poster, Endocrine Society member Sina Jasim, MD, from Washington University in St. Louis, Mo., and team started from the well-described data that cancers of the thyroid isthmus tend to have a higher risk of malignancy and more aggressive behavior than do lobar cancers and teased out some of the different molecular signatures occurring there.

These signatures, such as follicular to mesenchymal transition, provide mechanistic evidence of diagnostic and prognostic differences between isthmic and lobar tumors. Ultimately, using this molecular data may influence how isthmic thyroid cancer is managed. “The unique aspect of this platform allows us to find and/or create novel signatures,” Klopper explains.

Contrary Tumor Behavior

In summary, Klopper says, “Analyzing whole transcriptome–derived RNA sequencing provides a wealth of information. For the Afirma GSC test, we use this data to create benign and suspicious classifiers as our primary output, and they’re ‘trained to the truth’ — whether cancer is present or not.”

As we look toward the future where molecular testing can provide prognostic information, it must be recognized that even with the same mutation, thyroid cancers can behave very differently, so having additional molecular data may help clinicians provide more personalized care. Afirma GRID is a research use only tool that can allow for studies that analyze prognostic information beyond the presence of molecular variants and fusions.

Horvath is a Baltimore, Md.-based freelance writer. She wrote and researched the massive “Eureka 2023” in the December issue that highlighted the top endocrine discoveries of the year.