With NGS, new hope for managing thyroid nodules

Under the Bethesda National Cancer Institute reporting system for thyroid nodules, the indeterminate cytology encompasses three diagnostic subgroups. “One is this FLUS/AUS, with the lowest cancer risk, on average 15 percent. The second is FN/SFN [follicular or oncocytic neoplasm or suspicious for follicular neoplasm], and the last is SMC [suspicious for malignant cells]. Under the microscope, you can issue one of those three diagnoses, and each has different risks,” Dr. Nikiforov says.

“We know if they go for surgery, eight out of 10 patients with FLUS/AUS cytology will have a benign nodule, so surgery was not needed for those patients. These are the lowest-risk nodules, and yet because we cannot successfully diagnose cancer initially, most of those patients do go for surgery. Where we see a very big impact of mutational markers is on this group, because if these nodules are negative for all mutations, the risk of cancer is only six percent. It’s so low they don’t need to be operated on. They can be followed up on with periodic ultrasound examination. On the other hand, if a mutation is found, then the risk is 85 percent verified, and those patients should go for surgery.”

This recommendation was a fairly recent development, Dr. Nikiforov notes. “A new management algorithm was first proposed in 2011 based on a study we published in the Journal of Clinical Endocrinology & Metabolism, which allowed us to conclude that patients with FLUS/AUS and negative for all mutations can go without surgery.” So far, he says, that study is the largest to date on molecular markers and subsequent management of patients. It was a multidisciplinary effort, he says, led by a team of endocrinologists, endocrine surgeons, radiologists, cytopathologists, and molecular pathologists.

Right now, when patients come in and have FLUS/AUS cytology, most go for surgery. “It’s kind of like ‘one size fits all,’ but only 10 to 20 percent of these nodules are cancer. Using this new diagnostic tool, we can individualize the approach, recommending some for surgery, some for followup with ultrasound, and so on.”

For those patients diagnosed with thyroid cancer, an accepted management is that they have a complete thyroidectomy and radioactive iodine treatment. But radioactive iodine is a radiation treatment and has some risks. The majority of thyroid cancers are low-grade cancers, Dr. Nikiforov points out. “They’re very unlikely to recur and kill patients. Nonetheless, we treat all of them with aggressive therapy. Therefore, one other need for mutational markers is we must use them to separate, to identify only those thyroid cancers that are really aggressive and need to be further treated after surgical removal. For those that are not aggressive, we need an individualized approach—and that can be done with BRAF mutations plus additional markers we are developing.”

BRAF mutation correlates with a higher chance of recurrence and tumor-related death, he notes. “Treatment standards are now in development, but some patients with positive BRAF mutation found in the needle before surgery may benefit from more extensive surgery to be sure the tumor is removed completely. Those cancers that don’t have this mutation may not need radioactive iodine therapy.”

What remains to be explored? “The point mutations of the BRAF and three RAS genes and RET/PTC1, RET/PTC3, and PAX8/PPARgamma rearrangements are known to occur in approximately 70 to 75 percent of all thyroid cancers, which means there are still about 25 percent of cancers that don’t have mutations that can be detected by molecular markers. So this is a current limitation of this seven-marker panel.”

However, another 10 to 15 percent of cancers have less common known mutations. For example, TSHR mutations, BRAF rearrangements, and additional types of RET/PTC rearrangements are known to occur in well-differentiated thyroid cancers, and TP53, PIK3CA, and CTNNB1 mutations are known to occur in poorly differentiated and anaplastic carcinomas. “We know about those. But the problem is they occur in only about one to two percent of thyroid cancers.” For that reason, until recently it’s been difficult economically to test more than several markers, Dr. Nikiforov says. “It would become very expensive if every nodule were tested for all of these markers using the routine laboratory assays.” With the introduction of next-gen sequencing, this problem is resolved. “We have prepared a large panel to be run using NGS that will include not only the seven main mutations but all rare mutations that nevertheless occur in another 10 to 15 percent of cancers. So this addition will increase the sensitivity and specificity of cancer detection.”

Still remaining are about 10 to 15 percent of cancers that don’t have any known mutations. “Although most of them are very low-grade, indolent cancer, we still need to find markers for these tumors,” he says. “If you find those, then you create an ideal molecular test that will be able to accurately stratify all nodules with indeterminate cytology into either definitively benign or malignant.” Could such a test be developed? Dr. Nikiforov is optimistic. His laboratory is actively involved in whole-genome and whole-transcriptome sequencing of thyroid tumors with no known mutations, and The Cancer Genome Atlas (TCGA) is also sequencing 500 thyroid papillary cancers. “We expect that effort may also lead to the discovery of new mutational markers. In fact, we have already discovered several novel chromosomal rearrangements and point mutations in thyroid cancer that can be used as additional diagnostic markers.”

While some European publications have supported use of similar panels for diagnosis or as a marker for more aggressive carcinoma, the markers are not widely used in Europe, Dr. Nikiforov says. He believes the U.S. is in the vanguard in this effort.

“We currently routinely use seven mutational markers that identify 70 to 75 percent of tumors. Next, the NGS panel that we expect to introduce within two months will cover about 85 to 90 percent of cancers, including virtually all aggressive cancers. And my goal is to eliminate the uncertainty of indeterminate cytology from our care for patients with thyroid cancer.” At UPMC, first cytologic evaluation will be performed, then molecular tools applied to the 30 percent indeterminate to separate them into two groups, either benign or malignant, with high accuracy. “And that will tell our clinicians exactly how to manage those patients. Not only that, we will be able to predict how aggressive the patient’s cancer is, and how to treat it in a very individualized manner.”

Over the long term, Dr. Nikiforov believes virtually all mutations can be identified and put onto a molecular marker panel to test for thyroid cancer. “Now that we have the ability to use NGS to sequence the whole genome, we have a reasonable hope this will happen—and happen soon.”

Anne Paxton is a writer in Seattle.